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Peleke FF, Zumkeller SM, Gültas M, Schmitt A, Szymański J. Deep learning the cis-regulatory code for gene expression in selected model plants. Nat Commun 2024; 15:3488. [PMID: 38664394 PMCID: PMC11045779 DOI: 10.1038/s41467-024-47744-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Elucidating the relationship between non-coding regulatory element sequences and gene expression is crucial for understanding gene regulation and genetic variation. We explored this link with the training of interpretable deep learning models predicting gene expression profiles from gene flanking regions of the plant species Arabidopsis thaliana, Solanum lycopersicum, Sorghum bicolor, and Zea mays. With over 80% accuracy, our models enabled predictive feature selection, highlighting e.g. the significant role of UTR regions in determining gene expression levels. The models demonstrated remarkable cross-species performance, effectively identifying both conserved and species-specific regulatory sequence features and their predictive power for gene expression. We illustrated the application of our approach by revealing causal links between genetic variation and gene expression changes across fourteen tomato genomes. Lastly, our models efficiently predicted genotype-specific expression of key functional gene groups, exemplified by underscoring known phenotypic and metabolic differences between Solanum lycopersicum and its wild, drought-resistant relative, Solanum pennellii.
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Affiliation(s)
- Fritz Forbang Peleke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT, Gatersleben, Germany
| | - Simon Maria Zumkeller
- Institute of Bio- and Geosciences, IBG-4: Bioinformatics, Forschungszentrum Jülich, D-52428, Jülich, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Mehmet Gültas
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Soest, 59494, Germany
| | - Armin Schmitt
- Breeding Informatics Group, University of Göttingen, Göttingen, 37075, Germany
- Center of Integrated Breeding Research (CiBreed), Göttingen, 37075, Germany
| | - Jędrzej Szymański
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Seeland, OT, Gatersleben, Germany.
- Institute of Bio- and Geosciences, IBG-4: Bioinformatics, Forschungszentrum Jülich, D-52428, Jülich, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
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Soil Properties and Weed Dynamics in Wheat as Affected by Rice Residue Management in the Rice-Wheat Cropping System in South Asia: A Review. PLANTS 2021; 10:plants10050953. [PMID: 34068758 PMCID: PMC8151931 DOI: 10.3390/plants10050953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 11/20/2022]
Abstract
The rice–wheat cropping system (RWCS) has substantially contributed in making India self-sufficient in food grain production; however, rice residue management is of great concern, threatening the sustainability of this system. Rice residue is invariably disposed of by farmers through open burning. In addition to environmental pollution, residue burning of rice also leads to loss of soil nutrients. One of the alternatives to overcome these problems and sustain the RWCS is managing the rice residues in the field itself. Rice residue retention has variable effects on agricultural pests (namely, weeds, insect pests, diseases, and rodents) in the RWCS. High weed infestation in the RWCS results in high consumption of herbicides, which leads to several ecological problems and evolution of herbicide resistance. The shift from intensive tillage to conservation tillage causes major changes in weed dynamics and herbicide efficacy. Incorporation of rice residue reduces weed density and helps in improving soil physical, chemical, and biological properties. Rice residue retention on the surface or mulching reduces weed density and the biomass of both grass and broadleaf weeds in wheat crop as compared to its removal. Long-term field studies involving the use of rice residue as a component of integrated weed management strategies are needed to be done in the RWCS.
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Mellidou I, Koukounaras A, Kostas S, Patelou E, Kanellis AK. Regulation of Vitamin C Accumulation for Improved Tomato Fruit Quality and Alleviation of Abiotic Stress. Genes (Basel) 2021; 12:genes12050694. [PMID: 34066421 PMCID: PMC8148108 DOI: 10.3390/genes12050694] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/01/2021] [Accepted: 05/02/2021] [Indexed: 12/23/2022] Open
Abstract
Ascorbic acid (AsA) is an essential multifaceted phytonutrient for both the human diet and plant growth. Optimum levels of AsA accumulation combined with balanced redox homeostasis are required for normal plant development and defense response to adverse environmental stimuli. Notwithstanding its moderate AsA levels, tomatoes constitute a good source of vitamin C in the human diet. Therefore, the enhancement of AsA levels in tomato fruit attracts considerable attention, not only to improve its nutritional value but also to stimulate stress tolerance. Genetic regulation of AsA concentrations in plants can be achieved through the fine-tuning of biosynthetic, recycling, and transport mechanisms; it is also linked to changes in the whole fruit metabolism. Emerging evidence suggests that tomato synthesizes AsA mainly through the l-galactose pathway, but alternative pathways through d-galacturonate or myo-inositol, or seemingly unrelated transcription and regulatory factors, can be also relevant in certain developmental stages or in response to abiotic factors. Considering the recent advances in our understanding of AsA regulation in model and other non-model species, this review attempts to link the current consensus with novel technologies to provide a comprehensive strategy for AsA enhancement in tomatoes, without any detrimental effect on plant growth or fruit development.
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Affiliation(s)
- Ifigeneia Mellidou
- Institute of Plant Breeding and Genetic Resources, Hao Elgo-Demeter, 57001 Thessaloniki, Greece
- Correspondence: (I.M.); (A.K.K.)
| | - Athanasios Koukounaras
- Department of Horticulture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.K.); (S.K.)
| | - Stefanos Kostas
- Department of Horticulture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.K.); (S.K.)
| | - Efstathia Patelou
- Laboratory of Pharmacognosy, Group of Biotechnology of Pharmaceutical Plants, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Angelos K. Kanellis
- Laboratory of Pharmacognosy, Group of Biotechnology of Pharmaceutical Plants, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
- Correspondence: (I.M.); (A.K.K.)
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Sun S, Wang X, Wang K, Cui X. Dissection of complex traits of tomato in the post-genome era. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1763-1776. [PMID: 31745578 DOI: 10.1007/s00122-019-03478-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
We present the main advances of dissection of complex traits in tomato by omics, the genes identified to control complex traits and the application of CRISPR/Cas9 in tomato breeding. Complex traits are believed to be under the control of multiple genes, each with different effects and interaction with environmental factors. Advance development of sequencing and molecular technologies has enabled the recognition of the genomic structure of most organisms and the identification of a nearly limitless number of markers that have made it to accelerate the speed of QTL identification and gene cloning. Meanwhile, multiomics have been used to identify the genetic variations among different tomato species, determine the expression profiles of genes in different tissues and at distinct developmental stages, and detect metabolites in different pathways and processes. The combination of these data facilitates to reveal mechanism underlying complex traits. Moreover, mutants generated by mutagens and genome editing provide relatively rich genetic variation for deciphering the complex traits and exploiting them in tomato breeding. In this article, we present the main advances of complex trait dissection in tomato by omics since the release of the tomato genome sequence in 2012. We provide further insight into some tomato complex traits because of the causal genetic variations discovered so far and explore the utilization of CRISPR/Cas9 for the modification of tomato complex traits.
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Affiliation(s)
- Shuai Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaotian Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ketao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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D'Esposito D, Cappetta E, Andolfo G, Ferriello F, Borgonuovo C, Caruso G, De Natale A, Frusciante L, Ercolano MR. Deciphering the biological processes underlying tomato biomass production and composition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:50-60. [PMID: 31479882 DOI: 10.1016/j.plaphy.2019.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/19/2019] [Accepted: 08/13/2019] [Indexed: 05/20/2023]
Abstract
The huge amounts of biomass residues, remaining in the field after tomato fruits harvesting, can be utilized to produce bioenergy. A multiple level approach aimed to characterize two Solanum pennellii introgression lines (ILs), with contrasting phenotypes for plant architecture and biomass was carried out. The study of gene expression dynamics, microscopy cell traits and qualitative and quantitative cell wall chemical compounds variation enabled the discovery of key genes and cell processes involved biomass accumulation and composition. Enhanced biomass production observed in IL2-6 line is due to a more effective coordination of chloroplasts and mitochondria energy fluxes. Microscopy analysis revealed a higher number of cells and chloroplasts in leaf epidermis in the high biomass line whilst chemical measurements on the two lines pointed out striking differences in the cell wall composition and organization. Taken together, our findings shed light on the mechanisms underlying the tomato biomass production and processability.
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Affiliation(s)
- Daniela D'Esposito
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Elisa Cappetta
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Giuseppe Andolfo
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Francesca Ferriello
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Camilla Borgonuovo
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Gianluca Caruso
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Antonino De Natale
- Department of Biology, University of Naples 'Federico II', Via Cinthia, Monte Sant'Angelo, Building 7, 80126, Naples, Italy.
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Maria Raffaella Ercolano
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
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Biomass recalcitrance in barley, wheat and triticale straw: Correlation of biomass quality with classic agronomical traits. PLoS One 2018; 13:e0205880. [PMID: 30403701 PMCID: PMC6221549 DOI: 10.1371/journal.pone.0205880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/03/2018] [Indexed: 12/22/2022] Open
Abstract
The global production of cereal straw as an agricultural by-product presents a significant source of biomass, which could be used as feedstock for the production of second generation biofuels by fermentation. The production of sugars for fermentation is an important measure of straw quality and in its suitability for biofuel production. In this paper, we present a characterization of straw digestibility from a wide range of cereal. Our main objective is to evaluate the variability of fermentable sugars released from different species including wheat (Triticum durum L., Triticum aestivum L.), barley (Hordeum vulgare L.) and triticale (X Triticosecale Wittmack). To this end, we adapted a saccharification method (IAS Method) capable of detecting significant differences of released sugars between cultivars and species, while using separately another method that would serve as a control and with which we could contrast our results (CNAP method). ANOVA analyses revealed that barley has a higher saccharification potential than wheat and triticale and shows more variation between genotypes. Thus, populations derived from crosses among them such as Steptoe × Morex and OWB Dominant × OWB Recessive hold potential for the identification of genetic basis for saccharification-related traits. The correlation of glucose released between the two methods was moderate (R2 = 0.57). An evaluation of the inter- and intra- specific correlation between a number of chemical and agronomical parameters and saccharification suggests that the cell wall thickness and lignin content in straw could be used in breeding programs for the improvement of the saccharification potential. Finally, the lack of correlation between grain yield and saccharification suggests that it would be possible to make a selection of genotypes for dual purpose, low recalcitrance and grain yield.
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Galdon‐Armero J, Fullana‐Pericas M, Mulet PA, Conesa MA, Martin C, Galmes J. The ratio of trichomes to stomata is associated with water use efficiency in Solanum lycopersicum (tomato). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:607-619. [PMID: 30066411 PMCID: PMC6321981 DOI: 10.1111/tpj.14055] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 07/03/2018] [Accepted: 07/10/2018] [Indexed: 05/20/2023]
Abstract
Trichomes are specialised structures that originate from the aerial epidermis of plants, and play key roles in the interaction between the plant and the environment. In this study we investigated the trichome phenotypes of four lines selected from the Solanum lycopersicum × Solanum pennellii introgression line (IL) population for differences in trichome density, and their impact on plant performance under water-deficit conditions. We performed comparative analyses at morphological and photosynthetic levels of plants grown under well-watered (WW) and also under water-deficit (WD) conditions in the field. Under WD conditions, we observed higher trichome density in ILs 11-3 and 4-1, and lower stomatal size in IL 4-1 compared with plants grown under WW conditions. The intrinsic water use efficiency (WUEi ) was higher under WD conditions in IL 11-3, and the plant-level water use efficiency (WUEb ) was also higher in IL 11-3 and in M82 for WD plants. The ratio of trichomes to stomata (T/S) was positively correlated with WUEi and WUEb , indicating an important role for both trichomes and stomata in drought tolerance in tomato, and offering a promising way to select for improved water use efficiency of major crops.
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Affiliation(s)
| | - Mateu Fullana‐Pericas
- Research Group on Plant Biology under Mediterranean Conditions – INAGEAUniversitat de les Illes BalearsCarretera de Valldemossa km 7.507122PalmaSpain
| | - Pere A. Mulet
- Research Group on Plant Biology under Mediterranean Conditions – INAGEAUniversitat de les Illes BalearsCarretera de Valldemossa km 7.507122PalmaSpain
| | - Miquel A. Conesa
- Research Group on Plant Biology under Mediterranean Conditions – INAGEAUniversitat de les Illes BalearsCarretera de Valldemossa km 7.507122PalmaSpain
| | - Cathie Martin
- Department of Metabolic BiologyJohn Innes CentreColney LaneNorwichNR4 7UHUK
| | - Jeroni Galmes
- Research Group on Plant Biology under Mediterranean Conditions – INAGEAUniversitat de les Illes BalearsCarretera de Valldemossa km 7.507122PalmaSpain
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Rigano MM, Lionetti V, Raiola A, Bellincampi D, Barone A. Pectic enzymes as potential enhancers of ascorbic acid production through the D-galacturonate pathway in Solanaceae. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 266:55-63. [PMID: 29241567 DOI: 10.1016/j.plantsci.2017.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 10/19/2017] [Accepted: 10/23/2017] [Indexed: 05/24/2023]
Abstract
The increase of L-Ascorbic Acid (AsA) content in tomato (Solanum lycopersicum) is a common goal in breeding programs due to its beneficial effect on human health. To shed light into the regulation of fruit AsA content, we exploited a Solanum pennellii introgression line (IL12-4-SL) harbouring one quantitative trait locus that increases the content of total AsA in the fruit. Biochemical and transcriptomic analyses were carried out in fruits of IL12-4-SL in comparison with the cultivated line M82 at different stages of ripening. AsA content was studied in relation with pectin methylesterase (PME) activity and the degree of pectin methylesterification (DME). Our results indicated that the increase of AsA content in IL12-4-SL fruits was related with pectin de-methylesterification/degradation. Specific PME, polygalacturonase (PG) and UDP-D-glucuronic-acid-4-epimerase (UGlcAE) isoforms were proposed as components of the D-galacturonate pathway leading to AsA biosynthesis. The relationship between AsA content and PME activity was also exploited in PMEI tobacco plants expressing a specific PME inhibitor (PMEI). Here we report that tobacco PMEI plants, altered in PME activity and degree of pectin methylesterification, showed a reduction in low methylesterified pectic domains and exhibited a reduced AsA content. Overall, our results provide novel biochemical and genetic traits for increasing antioxidant content by marker-assisted selection in the Solanaceae family.
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Affiliation(s)
- Maria Manuela Rigano
- Department of Agricultural Sciences, University of Naples "Federico II", Via Università 100, 80055 Portici, Italy
| | - Vincenzo Lionetti
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Assunta Raiola
- Department of Agricultural Sciences, University of Naples "Federico II", Via Università 100, 80055 Portici, Italy
| | - Daniela Bellincampi
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy.
| | - Amalia Barone
- Department of Agricultural Sciences, University of Naples "Federico II", Via Università 100, 80055 Portici, Italy.
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Gramazio P, Prohens J, Plazas M, Mangino G, Herraiz FJ, Vilanova S. Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background. FRONTIERS IN PLANT SCIENCE 2017; 8:1477. [PMID: 28912788 PMCID: PMC5582342 DOI: 10.3389/fpls.2017.01477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/09/2017] [Indexed: 05/29/2023]
Abstract
Advanced backcrosses (ABs) and introgression lines (ILs) of eggplant (Solanum melongena) can speed up genetics and genomics studies and breeding in this crop. We have developed the first full set of ABs and ILs in eggplant using Solanum incanum, a wild eggplant that has a relatively high tolerance to drought, as a donor parent. The development of these ABs and IL eggplant populations had a low efficiency in the early stages, because of the lack of molecular markers and genomic tools. However, this dramatically improved after performing genotyping-by-sequencing in the first round of selfing, followed by high-resolution-melting single nucleotide polymorphism genotyping in subsequent selection steps. A set of 73 selected ABs covered 99% of the S. incanum genome, while 25 fixed immortal ILs, each carrying a single introgressed fragment in homozygosis, altogether spanned 61.7% of the S. incanum genome. The introgressed size fragment in the ILs contained between 0.1 and 10.9% of the S. incanum genome, with a mean value of 4.3%. Sixty-eight candidate genes involved in drought tolerance were identified in the set of ILs. This first set of ABs and ILs of eggplant will be extremely useful for the genetic dissection of traits of interest for eggplant, and represents an elite material for introduction into the breeding pipelines for developing new eggplant cultivars adapted to the challenges posed by the climate-change scenario.
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Affiliation(s)
- Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Mariola Plazas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politècnica de ValènciaValencia, Spain
| | - Giulio Mangino
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Francisco J. Herraiz
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
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