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M'hamdi O, Takács S, Palotás G, Ilahy R, Helyes L, Pék Z. A Comparative Analysis of XGBoost and Neural Network Models for Predicting Some Tomato Fruit Quality Traits from Environmental and Meteorological Data. PLANTS (BASEL, SWITZERLAND) 2024; 13:746. [PMID: 38475592 DOI: 10.3390/plants13050746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
The tomato as a raw material for processing is globally important and is pivotal in dietary and agronomic research due to its nutritional, economic, and health significance. This study explored the potential of machine learning (ML) for predicting tomato quality, utilizing data from 48 cultivars and 28 locations in Hungary over 5 seasons. It focused on °Brix, lycopene content, and colour (a/b ratio) using extreme gradient boosting (XGBoost) and artificial neural network (ANN) models. The results revealed that XGBoost consistently outperformed ANN, achieving high accuracy in predicting °Brix (R² = 0.98, RMSE = 0.07) and lycopene content (R² = 0.87, RMSE = 0.61), and excelling in colour prediction (a/b ratio) with a R² of 0.93 and RMSE of 0.03. ANN lagged behind particularly in colour prediction, showing a negative R² value of -0.35. Shapley additive explanation's (SHAP) summary plot analysis indicated that both models are effective in predicting °Brix and lycopene content in tomatoes, highlighting different aspects of the data. SHAP analysis highlighted the models' efficiency (especially in °Brix and lycopene predictions) and underscored the significant influence of cultivar choice and environmental factors like climate and soil. These findings emphasize the importance of selecting and fine-tuning the appropriate ML model for enhancing precision agriculture, underlining XGBoost's superiority in handling complex agronomic data for quality assessment.
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Affiliation(s)
- Oussama M'hamdi
- Institute of Horticultural Sciences, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100 Gödöllö, Hungary
- Doctoral School of Plant Science, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100 Gödöllö, Hungary
| | - Sándor Takács
- Institute of Horticultural Sciences, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100 Gödöllö, Hungary
| | - Gábor Palotás
- Univer Product Zrt, Szolnoki út 35, 6000 Kecskemét, Hungary
| | - Riadh Ilahy
- Laboratory of Horticulture, National Agricultural Research Institute of Tunisia (INRAT), University of Carthage, Ariana 1004, Tunisia
| | - Lajos Helyes
- Institute of Horticultural Sciences, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100 Gödöllö, Hungary
| | - Zoltán Pék
- Institute of Horticultural Sciences, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100 Gödöllö, Hungary
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2
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Zhang H, Zhao J, Zhang J, Wen S, Xie S, Yang S, Chen J, Zhou Y, Long G. Low-concentration exogenous 3-indoleacetic acid improves fruit-setting rate of Marsdenia tenacissima by inhibiting the expression of embryo abortion-related genes. Gene 2024; 893:147930. [PMID: 38381505 DOI: 10.1016/j.gene.2023.147930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/12/2023] [Accepted: 10/25/2023] [Indexed: 02/22/2024]
Abstract
Marsdenia tenacissima is a medicinal plant characterized by many flowers, few fruits, and a low fruit-setting rate. Exogenous auxins can improve the fruit-setting rate of plants; however, their impacts on M. tenacissima and regulatory mechanisms remain unclear. In this study, we conducted a field experiment to determine the fruit-setting rate, seed-setting rate, fruit size, and changes in transcriptional expression of related genes by spraying 10 and 50 mg·L-1 of 3-indoleacetic acid (IAA). The control plants were sprayed with distilled water. Our results indicated that the fruit-setting rate was 0.15 when treated with 10 mg·L-1 of IAA, which was 2.76-fold higher than that of the control. Compared with that of the control, the number of differentially expressed genes (DEGs) regulated by 10 mg·L-1 of IAA was 28.6-fold higher than that regulated by 50 mg·L-1 of IAA. These DEGs were closely related to hormone metabolism and fruit development. By transcriptome analysis, spraying 10 mg·L-1 of IAA increased the expressions of STP6, MYB17, and LAX3 and reduced those of CXE18, ILR1-like 3, and SAUR50; this possibly affected the ovule, embryo, and fruit development, thereby elevating the fruit-setting rate of M. tenacissima. Our results indicated that low IAA concentration increased the fruit-setting rate of M. tenacissima, providing theoretical and practical support for promoting the seed yield of M. tenacissima.
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Affiliation(s)
- Haoyue Zhang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
| | - Jiuxia Zhao
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
| | - Jingling Zhang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
| | - Shuhan Wen
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
| | - Shiqing Xie
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Shengchao Yang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Junwen Chen
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Yanli Zhou
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Guangqiang Long
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan 650201, China.
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3
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Daloso DDM, Morais EG, Oliveira E Silva KF, Williams TCR. Cell-type-specific metabolism in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1093-1114. [PMID: 36987968 DOI: 10.1111/tpj.16214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/20/2023] [Accepted: 03/25/2023] [Indexed: 05/31/2023]
Abstract
Every plant organ contains tens of different cell types, each with a specialized function. These functions are intrinsically associated with specific metabolic flux distributions that permit the synthesis of the ATP, reducing equivalents and biosynthetic precursors demanded by the cell. Investigating such cell-type-specific metabolism is complicated by the mosaic of different cells within each tissue combined with the relative scarcity of certain types. However, techniques for the isolation of specific cells, their analysis in situ by microscopy, or modeling of their function in silico have permitted insight into cell-type-specific metabolism. In this review we present some of the methods used in the analysis of cell-type-specific metabolism before describing what we know about metabolism in several cell types that have been studied in depth; (i) leaf source and sink cells; (ii) glandular trichomes that are capable of rapid synthesis of specialized metabolites; (iii) guard cells that must accumulate large quantities of the osmolytes needed for stomatal opening; (iv) cells of seeds involved in storage of reserves; and (v) the mesophyll and bundle sheath cells of C4 plants that participate in a CO2 concentrating cycle. Metabolism is discussed in terms of its principal features, connection to cell function and what factors affect the flux distribution. Demand for precursors and energy, availability of substrates and suppression of deleterious processes are identified as key factors in shaping cell-type-specific metabolism.
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Affiliation(s)
- Danilo de Menezes Daloso
- Lab Plant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CA, 60451-970, Brazil
| | - Eva Gomes Morais
- Lab Plant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CA, 60451-970, Brazil
| | - Karen Fernanda Oliveira E Silva
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília-DF, 70910-900, Brazil
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Suttiyut T, Benzinger SW, McCoy RM, Widhalm JR. Strategies to study the metabolic origins of specialized plant metabolites: The specialized 1,4-naphthoquinones. Methods Enzymol 2023; 680:217-246. [PMID: 36710012 DOI: 10.1016/bs.mie.2022.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
One of the hallmarks of specialized plant metabolites is that they are produced using precursors from central metabolism. Therefore, in addition to identifying and characterizing the pathway genes and enzymes involved in synthesizing a specialized compound, it is critical to study its metabolic origins. Identifying what primary metabolic pathways supply precursors to specialized metabolism and how primary metabolism has diversified to sustain fluxes to specialized metabolite pathways is imperative to optimizing synthetic biology strategies for producing high-value plant natural products in crops and microbial systems. Improved understanding of the metabolic origins of specialized plant metabolites has also revealed instances of recurrent evolution of the same compound, or nearly identical compounds, with similar ecological functions, thereby expanding knowledge about the factors driving the chemical diversity in the plant kingdom. In this chapter, we describe detailed methods for performing tracer studies, chemical inhibitor experiments, and reverse genetics. We use examples from investigations of the metabolic origins of specialized plant 1,4-naphthoquinones (1,4-NQs). The plant 1,4-NQs provide an excellent case study for illustrating the importance of investigating the metabolic origins of specialized metabolites. Over half a century of research by many groups has revealed that the pathways to synthesize plant 1,4-NQs are the result of multiple events of convergent evolution across several disparate plant lineages and that plant 1,4-NQ pathways are supported by extraordinary events of metabolic innovation and by various primary metabolic sources.
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Affiliation(s)
- Thiti Suttiyut
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Scott W Benzinger
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Rachel M McCoy
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States.
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5
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Bhandari P, Kim J, Lee TG. Genetic architecture of fresh-market tomato yield. BMC PLANT BIOLOGY 2023; 23:18. [PMID: 36624387 PMCID: PMC9827693 DOI: 10.1186/s12870-022-04018-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The fresh-market tomato (Solanum lycopersicum) is bred for direct consumption and is selected for a high yield of large fruits. To understand the genetic variations (distinct types of DNA sequence polymorphism) that influence the yield, we collected the phenotypic variations in the yields of total fruit, extra-large-sized fruit, small-sized fruit, or red-colored fruit from 68 core inbred contemporary U.S. fresh-market tomatoes for three consecutive years and the genomic information in 8,289,741 single nucleotide polymorphism (SNP) positions from the whole-genome resequencing of these tomatoes. RESULTS Genome-wide association (GWA) mapping using the SNP data with or without SNP filtering steps using the regularization methods, validated with quantitative trait loci (QTL) linkage mapping, identified 18 significant association signals for traits evaluated. Among them, 10 of which were not located within genomic regions previously identified as being associated with fruit size/shape. When mapping-driven association signals [558 SNPs associated with 28 yield (component) traits] were used to calculate genomic estimated breeding values (GEBVs) of evaluated traits, the prediction accuracies of the extra-large-sized fruit and small-sized fruit yields were higher than those of the total and red-colored fruit yields, as we tested the generated breeding values in inbred tomatoes and F2 populations. Improved accuracy in GEBV calculation of evaluated traits was achieved by using 364 SNPs identified using the regularization methods. CONCLUSIONS Together, these results provide an understanding of the genetic variations underlying the heritable phenotypic variability in yield in contemporary tomato breeding and the information necessary for improving such economically important and complex quantitative trait through breeding.
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Affiliation(s)
- Prashant Bhandari
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Juhee Kim
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, USA
| | - Tong Geon Lee
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, USA.
- Plant Breeders Working Group, University of Florida, Gainesville, FL, 32611, USA.
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, 32611, USA.
- Bayer, Chesterfield, MO, 63017, USA.
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Rosado-Souza L, Yokoyama R, Sonnewald U, Fernie AR. Understanding source-sink interactions: Progress in model plants and translational research to crops. MOLECULAR PLANT 2023; 16:96-121. [PMID: 36447435 DOI: 10.1016/j.molp.2022.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/25/2022] [Indexed: 06/16/2023]
Abstract
Agriculture is facing a massive increase in demand per hectare as a result of an ever-expanding population and environmental deterioration. While we have learned much about how environmental conditions and diseases impact crop yield, until recently considerably less was known concerning endogenous factors, including within-plant nutrient allocation. In this review, we discuss studies of source-sink interactions covering both fundamental research in model systems under controlled growth conditions and how the findings are being translated to crop plants in the field. In this respect we detail efforts aimed at improving and/or combining C3, C4, and CAM modes of photosynthesis, altering the chloroplastic electron transport chain, modulating photorespiration, adopting bacterial/algal carbon-concentrating mechanisms, and enhancing nitrogen- and water-use efficiencies. Moreover, we discuss how modulating TCA cycle activities and primary metabolism can result in increased rates of photosynthesis and outline the opportunities that evaluating natural variation in photosynthesis may afford. Although source, transport, and sink functions are all covered in this review, we focus on discussing source functions because the majority of research has been conducted in this field. Nevertheless, considerable recent evidence, alongside the evidence from classical studies, demonstrates that both transport and sink functions are also incredibly important determinants of yield. We thus describe recent evidence supporting this notion and suggest that future strategies for yield improvement should focus on combining improvements in each of these steps to approach yield optimization.
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Affiliation(s)
- Laise Rosado-Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Ryo Yokoyama
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Uwe Sonnewald
- Department of Biochemistry, University of Erlangen-Nuremberg, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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Zhu F, Jadhav SS, Tohge T, Salem MA, Lee JM, Giovannoni JJ, Cheng Y, Alseekh S, Fernie AR. A comparative transcriptomics and eQTL approach identifies SlWD40 as a tomato fruit ripening regulator. PLANT PHYSIOLOGY 2022; 190:250-266. [PMID: 35512210 PMCID: PMC9434188 DOI: 10.1093/plphys/kiac200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/28/2022] [Indexed: 05/31/2023]
Abstract
Although multiple vital genes with strong effects on the tomato (Solanum lycopersicum) ripening process have been identified via the positional cloning of ripening mutants and cloning of ripening-related transcription factors (TFs), recent studies suggest that it is unlikely that we have fully characterized the gene regulatory networks underpinning this process. Here, combining comparative transcriptomics and expression QTLs, we identified 16 candidate genes involved in tomato fruit ripening and validated them through virus-induced gene silencing analysis. To further confirm the accuracy of the approach, one potential ripening regulator, SlWD40 (WD-40 repeats), was chosen for in-depth analysis. Co-expression network analysis indicated that master regulators such as RIN (ripening inhibitor) and NOR (nonripening) as well as vital TFs including FUL1 (FRUITFUL1), SlNAC4 (NAM, ATAF1,2, and CUC2 4), and AP2a (Activating enhancer binding Protein 2 alpha) strongly co-expressed with SlWD40. Furthermore, SlWD40 overexpression and RNAi lines exhibited substantially accelerated and delayed ripening phenotypes compared with the wild type, respectively. Moreover, transcriptome analysis of these transgenics revealed that expression patterns of ethylene biosynthesis genes, phytoene synthase, pectate lyase, and branched chain amino transferase 2, in SlWD40-RNAi lines were similar to those of rin and nor fruits, which further demonstrated that SlWD40 may act as an important ripening regulator in conjunction with RIN and NOR. These results are discussed in the context of current models of ripening and in terms of the use of comparative genomics and transcriptomics as an effective route for isolating causal genes underlying differences in genotypes.
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Affiliation(s)
| | | | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Mohamed A Salem
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University, Menoufia 32511, Egypt
| | | | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
- US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Yunjiang Cheng
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Song M, Zhang X, Yang J, Gao C, Wei Y, Chen S, Liesche J. Arabidopsis plants engineered for high root sugar secretion enhance the diversity of soil microorganisms. Biotechnol J 2022; 17:e2100638. [PMID: 35894173 DOI: 10.1002/biot.202100638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/06/2022]
Abstract
Plants secrete sugars from their roots into the soil, presumably to support beneficial plant-microbe interactions. Accordingly, manipulation of sugar secretion might be a viable strategy to enhance plant health and productivity. To evaluate the effect of increased root sugar secretion on plant performance and the soil microbiome, we overexpressed glucose and sucrose-specific membrane transporters in root epidermal cells of the model plant Arabidopsis thaliana. These plants showed strongly increased rates of sugar secretion in a hydroponic culture system. When grown on soil, the transporter-overexpressor plants displayed a higher photosynthesis rate, but reduced shoot growth compared to the wild-type control. Amplicon sequencing and qPCR analysis of rhizosphere soil samples indicated a limited effect on the total abundance of bacteria and fungi, but a strong effect on community structure in soil samples associated with the overexpressors. Notable changes included the increased abundance of bacteria belonging to the genus Rhodanobacter and the fungi belonging to the genus Cutaneotrichosporon, while Candida species abundance was reduced. The potential influences of the altered soil microbiome on plant health and productivity are discussed. The results indicate that the engineering of sugar secretion can be a viable pathway to enhancing the carbon sequestration rate and optimizing the soil microbiome. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Min Song
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,Biomass Energy Center for Arid and Semiarid Lands, Northwest A&F University, Yangling, 712100, China.,State Key Laboratory of Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Xingjian Zhang
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,Biomass Energy Center for Arid and Semiarid Lands, Northwest A&F University, Yangling, 712100, China.,State Key Laboratory of Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Jintao Yang
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,Biomass Energy Center for Arid and Semiarid Lands, Northwest A&F University, Yangling, 712100, China.,State Key Laboratory of Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Chen Gao
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark
| | - Yahong Wei
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,Biomass Energy Center for Arid and Semiarid Lands, Northwest A&F University, Yangling, 712100, China
| | - Shaolin Chen
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,Biomass Energy Center for Arid and Semiarid Lands, Northwest A&F University, Yangling, 712100, China
| | - Johannes Liesche
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,Biomass Energy Center for Arid and Semiarid Lands, Northwest A&F University, Yangling, 712100, China.,State Key Laboratory of Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
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Development of a facile genetic transformation system for the Spanish elite rice paella genotype Bomba. Transgenic Res 2022; 31:325-340. [PMID: 35416603 PMCID: PMC9135871 DOI: 10.1007/s11248-022-00303-z] [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: 01/13/2022] [Accepted: 03/11/2022] [Indexed: 11/17/2022]
Abstract
We report the development of an efficient and reproducible genetic transformation system for the recalcitrant Spanish elite rice paella genotype, Bomba. Preconditioned embryos derived from dry seeds were bombarded with gold particles carrying a plasmid containing a screenable and a selectable marker. We confirmed integration and expression of hpt and gusA in the rice genome. Transformation frequency was ca: 10% in several independent experiments. We show Mendelian inheritance of the input transgenes and zygosity determination of the transgenic lines in the T1 generation. A unique and critical step for the regeneration of plants from transformed tissue was shading during the early stages of regeneration, combined with a specific cytokinin:auxin ration at the onset of shifting callus to regeneration media.
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Choudhary A, Kumar A, Kaur N, Kaur H. Molecular cues of sugar signaling in plants. PHYSIOLOGIA PLANTARUM 2022; 174:e13630. [PMID: 35049040 DOI: 10.1111/ppl.13630] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/02/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Sugars, the chemically bound form of energy, are formed by the absorption of photosynthetically active radiation and fixation in plants. During evolution, plants availed the sugar molecules as a resource, balancing molecule, and signaling molecule. The multifaceted role of sugar molecules in response to environmental stimuli makes it the central coordinator required for growth, survival, and continuity. During the course of evolution, the molecular networks have become complex to adapt or acclimate to the changing environment. Sugar molecules are sensed both intra and extracellularly by their specific sensors. The signal is transmitted by a signaling loop that involves various downstream signaling molecules, transcriptional factors and, most pertinent, the sensors TOR and SnRK1. In this review, the focus has been retained on the significance of the sugar sensors during signaling and induced modules to regulate plant growth, development, biotic and abiotic stress. It is interesting to visualize the sugar molecule as a signaling unit and not only a nutrient. Complete information on the downstream components of sugar signaling will open the gates for improving the qualitative and quantitative elements of crop plants.
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Affiliation(s)
- Anuj Choudhary
- Department of Botany, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Antul Kumar
- Department of Botany, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Nirmaljit Kaur
- Department of Botany, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Harmanjot Kaur
- Department of Botany, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Punjab, India
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11
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Paul MJ. What are the regulatory targets for intervention in assimilate partitioning to improve crop yield and resilience? JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153537. [PMID: 34619557 DOI: 10.1016/j.jplph.2021.153537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Sucrose utilisation for the synthesis of cellular components involved in growth and development and the accumulation of biomass determines diversity in the plant kingdom; sucrose utilisation and partitioning also underpin crop yields. As a complex process the use of sucrose for the partitioning of plant products for yield is decided by the interaction of several regulatory hubs and the integration of metabolism and development. Understanding the regulation of assimilate partitioning has been a grand challenge in plant and crop science. There are emerging examples of genes and processes that appear important for assimilate partitioning that underpin yield in crops and which are amenable to intervention. Enzymes of carbon metabolism were some of the first targets in attempts to modify assimilate partitioning at the beginning (source) and end (sink) of the whole plant assimilate partitioning process. Metabolic enzymes are subject to regulatory and homeostatic mechanisms, a key factor to consider in modifying assimilate partitioning. Trehalose 6-phosphate, as a sucrose signal, may represent a special case in its ability to regulate and coordinate source and sink processes. This review summarises recent progress in understanding the underlying regulators of assimilate partitioning and the current and potentially most promising routes to crop yield enhancement with a main focus on cereals. A framework for how source-sink may regulate whole plant assimilate partitioning involving a few key elements and the central importance of reproductive development is presented.
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Affiliation(s)
- Matthew J Paul
- Plant Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
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Durán-Soria S, Pott DM, Will F, Mesa-Marín J, Lewandowski M, Celejewska K, Masny A, Żurawicz E, Jennings N, Sønsteby A, Krüger E, Osorio S. Exploring Genotype-by-Environment Interactions of Chemical Composition of Raspberry by Using a Metabolomics Approach. Metabolites 2021; 11:metabo11080490. [PMID: 34436431 PMCID: PMC8398420 DOI: 10.3390/metabo11080490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022] Open
Abstract
Promoting the consumption of fruits is a key objective of nutrition policy campaigns due to their associated health benefits. Raspberries are well appreciated for their remarkable flavor and nutritional value attributable to their antioxidant properties. Consequently, one of the objectives of present-day raspberry breeding programs is to improve the fruit’s sensory and nutritive characteristics. However, developing new genotypes with enhanced quality traits is a complex task due to the intricate impacts genetic and environmental factors have on these attributes, and the difficulty to phenotype them. We used a multi-platform metabolomic approach to compare flavor- and nutritional-related metabolite profiles of four raspberry cultivars (‘Glen Ample’, ‘Schönemann’, ‘Tulameen’ and ‘Veten’) grown in different European climates. Although the cultivars appear to be better adapted to high latitudes, for their content in soluble solids and acidity, multivariate statistical analyses allowed us to underscore important genotypic differences based on the profiles of important metabolites. ‘Schönemann’ and ‘Veten’ were characterized by high levels of anthocyanins and ellagitannins, respectively, ‘Tulameen’ by its acidity, and ‘Glen Ample’ for its content of sucrose and β-ionone, two main flavor contributors. Our results confirmed the value of metabolomic-driven approaches, which may foster the development of cultivars with enhanced health properties and flavor.
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Affiliation(s)
- Sara Durán-Soria
- Departamento de Biología Molecular y Bioquímica, Campus de Teatinos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain; (S.D.-S.); (D.M.P.); (J.M.-M.)
| | - Delphine M. Pott
- Departamento de Biología Molecular y Bioquímica, Campus de Teatinos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain; (S.D.-S.); (D.M.P.); (J.M.-M.)
| | - Frank Will
- Institute of Beverage Research, Hochschule Geisenheim University, 65366 Geisenheim, Germany;
| | - Jennifer Mesa-Marín
- Departamento de Biología Molecular y Bioquímica, Campus de Teatinos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain; (S.D.-S.); (D.M.P.); (J.M.-M.)
| | - Mariusz Lewandowski
- The National Institute of Horticultural Research (INHORT), Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; (M.L.); (K.C.); (A.M.)
| | - Karolina Celejewska
- The National Institute of Horticultural Research (INHORT), Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; (M.L.); (K.C.); (A.M.)
| | - Agnieszka Masny
- The National Institute of Horticultural Research (INHORT), Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; (M.L.); (K.C.); (A.M.)
| | - Edward Żurawicz
- The National Institute of Horticultural Research (INHORT), Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; (M.L.); (K.C.); (A.M.)
| | - Nikki Jennings
- Department of Genetics, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK;
| | - Anita Sønsteby
- NIBIO, Norwegian Institute of Bioeconomy Research, 1431 Ås, Norway;
| | - Erika Krüger
- Institute of Pomology, Hochschule Geisenheim University, 65366 Geisenheim, Germany;
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Campus de Teatinos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain; (S.D.-S.); (D.M.P.); (J.M.-M.)
- Correspondence: ; Tel.: +34-952-132-394
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