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Ma H, Pei J, Zhuo J, Tang Q, Hou D, Lin X. The CONSTANS-LIKE gene PeCOL13 regulates flowering through intron-retained alternative splicing in Phyllostachys edulis. Int J Biol Macromol 2024; 274:133393. [PMID: 38917922 DOI: 10.1016/j.ijbiomac.2024.133393] [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: 05/07/2024] [Revised: 06/14/2024] [Accepted: 06/22/2024] [Indexed: 06/27/2024]
Abstract
Woody bamboo exhibits a unique flowering characteristic with a lengthy flowering cycle, often followed by death. In many plant species, alternative splicing (AS) is a common phenomenon involved in controlling flowering. In this study, a PeCOL13 gene in moso bamboo (Phyllostachys edulis) was characterized. It produced two isoforms: PeCOL13α and PeCOL13β, due to an intron-retained AS. The PeCOL13α expressed in the vegetative phase and the reproductive phase, but the PeCOL13β didn't express during the vegetative phase and showed only a weak expression from F1 to F3 during the reproductive phase. Overexpression of PeCOL13α in rice (Oryza sativa) resulted in a delayed heading time through inhibiting the expressions of Hd3a, OsFTL1, and Ehd1 and activating the expressions of Ghd7 and RCN1. However, the PeCOL13β-overexpressed rice didn't show any significant differences in flowering compared with wild-type (WT), and the expressions of downstream flowering genes had no notable changes. Further analysis revealed that both PeCOL13α and PeCOL13β can bind to the PeFT promoter. Meanwhile, PeCOL13α can inhibit the transcription of PeFT, but PeCOL13β showed no effect. When PeCOL13α and PeCOL13β coexist, the inhibitory effect of PeCOL13α on PeFT transcription was weakened by PeCOL13β. This study provides new insights into the mechanism of bamboo flowering research.
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Affiliation(s)
- Hongjia Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin' an 311300, China; Bamboo Industry Institute, Zhejiang A&F University, Lin' an 311300, China
| | - Jialong Pei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin' an 311300, China; Bamboo Industry Institute, Zhejiang A&F University, Lin' an 311300, China
| | - Juan Zhuo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin' an 311300, China; Bamboo Industry Institute, Zhejiang A&F University, Lin' an 311300, China
| | - Qingyun Tang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin' an 311300, China; Bamboo Industry Institute, Zhejiang A&F University, Lin' an 311300, China
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin' an 311300, China; Bamboo Industry Institute, Zhejiang A&F University, Lin' an 311300, China.
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin' an 311300, China; Bamboo Industry Institute, Zhejiang A&F University, Lin' an 311300, China.
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Gao Y, Zhou S, Huang Y, Zhang B, Xu Y, Zhang G, Lakshmanan P, Yang R, Zhou H, Huang D, Liu J, Tan H, He W, Yang C, Duan W. Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane ( Saccharum spp.). FRONTIERS IN PLANT SCIENCE 2022; 12:796189. [PMID: 35069651 PMCID: PMC8766830 DOI: 10.3389/fpls.2021.796189] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/13/2021] [Indexed: 06/02/2023]
Abstract
Sugarcane is one of the most important industrial crops globally. It is the second largest source of bioethanol, and a major crop for biomass-derived electricity and sugar worldwide. Smut, caused by Sporisorium scitamineum, is a major sugarcane disease in many countries, and is managed by smut-resistant varieties. In China, smut remains the single largest constraint for sugarcane production, and consequently it impacts the value of sugarcane as an energy feedstock. Quantitative trait loci (QTLs) associated with smut resistance and linked diagnostic markers are valuable tools for smut resistance breeding. Here, we developed an F1 population (192 progeny) by crossing two sugarcane varieties with contrasting smut resistance and used for genome-wide single nucleotide polymorphism (SNP) discovery and mapping, using a high-throughput genotyping method called "specific locus amplified fragment sequencing (SLAF-seq) and bulked-segregant RNA sequencing (BSR-seq). SLAF-seq generated 148,500 polymorphic SNP markers. Using SNP and previously identified SSR markers, an integrated genetic map with an average 1.96 cM marker interval was produced. With this genetic map and smut resistance scores of the F1 individuals from four crop years, 21 major QTLs were mapped, with a phenotypic variance explanation (PVE) > 8.0%. Among them, 10 QTLs were stable (repeatable) with PVEs ranging from 8.0 to 81.7%. Further, four QTLs were detected based on BSR-seq analysis. aligning major QTLs with the genome of a sugarcane progenitor Saccharum spontaneum, six markers were found co-localized. Markers located in QTLs and functional annotation of BSR-seq-derived unigenes helped identify four disease resistance candidate genes located in major QTLs. 77 SNPs from major QTLs were then converted to Kompetitive Allele-Specific PCR (KASP) markers, of which five were highly significantly linked to smut resistance. The co-localized QTLs, candidate resistance genes, and KASP markers identified in this study provide practically useful tools for marker-assisted sugarcane smut resistance breeding.
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Affiliation(s)
- Yijing Gao
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Shan Zhou
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Yuxin Huang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Baoqing Zhang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, China
| | - Gemin Zhang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Prakash Lakshmanan
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, China
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | - Rongzhong Yang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Hui Zhou
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Dongliang Huang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Junxian Liu
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Hongwei Tan
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Weizhong He
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Cuifang Yang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Weixing Duan
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
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Ramasamy M, Damaj MB, Vargas-Bautista C, Mora V, Liu J, Padilla CS, Irigoyen S, Saini T, Sahoo N, DaSilva JA, Mandadi KK. A Sugarcane G-Protein-Coupled Receptor, ShGPCR1, Confers Tolerance to Multiple Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:745891. [PMID: 35295863 PMCID: PMC8919185 DOI: 10.3389/fpls.2021.745891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/14/2021] [Indexed: 06/14/2023]
Abstract
Sugarcane (Saccharum spp.) is a prominent source of sugar and serves as bioenergy/biomass feedstock globally. Multiple biotic and abiotic stresses, including drought, salinity, and cold, adversely affect sugarcane yield. G-protein-coupled receptors (GPCRs) are components of G-protein-mediated signaling affecting plant growth, development, and stress responses. Here, we identified a GPCR-like protein (ShGPCR1) from sugarcane and energy cane (Saccharum spp. hybrids) and characterized its function in conferring tolerance to multiple abiotic stresses. ShGPCR1 protein sequence contained nine predicted transmembrane (TM) domains connected by four extracellular and four intracellular loops, which could interact with various ligands and heterotrimeric G proteins in the cells. ShGPCR1 sequence displayed other signature features of a GPCR, such as a putative guanidine triphosphate (GTP)-binding domain, as well as multiple myristoylation and protein phosphorylation sites, presumably important for its biochemical function. Expression of ShGPCR1 was upregulated by drought, salinity, and cold stresses. Subcellular imaging and calcium (Ca2+) measurements revealed that ShGPCR1 predominantly localized to the plasma membrane and enhanced intracellular Ca2+ levels in response to GTP, respectively. Furthermore, constitutive overexpression of ShGPCR1 in sugarcane conferred tolerance to the three stressors. The stress-tolerance phenotype of the transgenic lines corresponded with activation of multiple drought-, salinity-, and cold-stress marker genes, such as Saccharum spp. LATE EMBRYOGENESIS ABUNDANT, DEHYDRIN, DROUGHT RESPONSIVE 4, GALACTINOL SYNTHASE, ETHYLENE RESPONSIVE FACTOR 3, SALT OVERLY SENSITIVE 1, VACUOLAR Na+/H+ ANTIPORTER 1, NAM/ATAF1/2/CUC2, COLD RESPONSIVE FACTOR 2, and ALCOHOL DEHYDROGENASE 3. We suggest that ShGPCR1 plays a key role in conferring tolerance to multiple abiotic stresses, and the engineered lines may be useful to enhance sugarcane production in marginal environments with fewer resources.
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Affiliation(s)
- Manikandan Ramasamy
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Mona B. Damaj
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | | | - Victoria Mora
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Jiaxing Liu
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Carmen S. Padilla
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Tripti Saini
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, TX, United States
| | - Nirakar Sahoo
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, TX, United States
| | - Jorge A. DaSilva
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Kranthi K. Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
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Vuletin Selak G, Baruca Arbeiter A, Cuevas J, Perica S, Pujic P, Raboteg Božiković M, Bandelj D. Seed Paternity Analysis Using SSR Markers to Assess Successful Pollen Donors in Mixed Olive Orchards. PLANTS 2021; 10:plants10112356. [PMID: 34834719 PMCID: PMC8624852 DOI: 10.3390/plants10112356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/19/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022]
Abstract
The olive tree (Olea europaea L.) is a wind-pollinated crop that exhibits an extreme alternate bearing habit. To improve fruit set, several methods have been used to determine the most successful compatible combinations of cultivars. In this study, priority is given to seed paternity analysis based on simple sequence repeats (SSRs), microsatellite markers used for the identification of potential pollen donors of cultivar ‘Oblica’ in a mixed olive orchard during two consecutive years. Seven microsatellite primers were successfully used to examine the paternity of olive embryos from ‘Oblica’ mother trees. Embryos were considered as a product of self-fertilization if only maternal alleles were present, but not a single case of self-fertilization was found among all the embryos analyzed. Two dominant pollen donors were not the closest nor the cultivars with the highest number of trees in the orchard, suggesting that cross-compatibility may have a key role in determining pollen donor success. In our earlier studies, pollen tube growth and fertilization success correlated with fruit set when controlled crosses between cultivars were performed; however, some discrepancy might appear compared to paternity analyses when mother trees have a free choice among different pollen sources from cultivars growing in their surroundings.
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Affiliation(s)
- Gabriela Vuletin Selak
- Department of Plant Sciences, Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia; (S.P.); (M.R.B.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska Cesta 25, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-21-434-436
| | - Alenka Baruca Arbeiter
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, 6000 Koper, Slovenia; (A.B.A.); (D.B.)
| | - Julián Cuevas
- Department of Agronomy, University of Almería, CeiA3, La Cañada de San Urbano, s/n, 04120 Almería, Spain;
| | - Slavko Perica
- Department of Plant Sciences, Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia; (S.P.); (M.R.B.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska Cesta 25, 10000 Zagreb, Croatia
| | - Petar Pujic
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622 Villeurbanne, France;
| | - Marina Raboteg Božiković
- Department of Plant Sciences, Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia; (S.P.); (M.R.B.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska Cesta 25, 10000 Zagreb, Croatia
| | - Dunja Bandelj
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, 6000 Koper, Slovenia; (A.B.A.); (D.B.)
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Padilla CS, Damaj MB, Yang ZN, Molina J, Berquist BR, White EL, Solís-Gracia N, Da Silva J, Mandadi KK. High-Level Production of Recombinant Snowdrop Lectin in Sugarcane and Energy Cane. Front Bioeng Biotechnol 2020; 8:977. [PMID: 33015000 PMCID: PMC7461980 DOI: 10.3389/fbioe.2020.00977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/27/2020] [Indexed: 01/11/2023] Open
Abstract
Sugarcane and energy cane (Saccharum spp. hybrids) are ideal for plant-based production of recombinant proteins because their high resource-use efficiency, rapid growth and efficient photosynthesis enable extensive biomass production and protein accumulation at a cost-effective scale. Here, we aimed to develop these species as efficient platforms to produce recombinant Galanthus nivalis L. (snowdrop) agglutinin (GNA), a monocot-bulb mannose-specific lectin with potent antiviral, antifungal and antitumor activities. Initially, GNA levels of 0.04% and 0.3% total soluble protein (TSP) (0.3 and 3.8 mg kg–1 tissue) were recovered from the culms and leaves, respectively, of sugarcane lines expressing recombinant GNA under the control of the constitutive maize ubiquitin 1 (Ubi) promoter. Co-expression of recombinant GNA from stacked multiple promoters (pUbi and culm-regulated promoters from sugarcane dirigent5-1 and Sugarcane bacilliform virus) on separate expression vectors increased GNA yields up to 42.3-fold (1.8% TSP or 12.7 mg kg–1 tissue) and 7.7-fold (2.3% TSP or 29.3 mg kg–1 tissue) in sugarcane and energy cane lines, respectively. Moreover, inducing promoter activity in the leaves of GNA transgenic lines with stress-regulated hormones increased GNA accumulation to 2.7% TSP (37.2 mg kg–1 tissue). Purification by mannose-agarose affinity chromatography yielded a functional sugarcane recombinant GNA with binding substrate specificity similar to that of native snowdrop-bulb GNA, as shown by enzyme-linked lectin and mannose-binding inhibition assays. The size and molecular weight of recombinant GNA were identical to those of native GNA, as determined by size-exclusion chromatography and MALDI-TOF mass spectrometry. This work demonstrates the feasibility of producing recombinant GNA at high levels in Saccharum species, with the long-term goal of using it as a broad-spectrum antiviral carrier molecule for hemopurifiers and in related therapeutic applications.
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Affiliation(s)
- Carmen S Padilla
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Mona B Damaj
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Zhong-Nan Yang
- Institute for Plant Gene Function, Department of Biology, Shanghai Normal University, Shanghai, China
| | - Joe Molina
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | | | - Earl L White
- MDx BioAnalytical Laboratory, Inc., College Station, TX, United States
| | - Nora Solís-Gracia
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Jorge Da Silva
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States.,Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States.,Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
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Sanchez L, Pant S, Mandadi K, Kurouski D. Raman Spectroscopy vs Quantitative Polymerase Chain Reaction In Early Stage Huanglongbing Diagnostics. Sci Rep 2020; 10:10101. [PMID: 32572139 PMCID: PMC7308309 DOI: 10.1038/s41598-020-67148-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/03/2020] [Indexed: 12/21/2022] Open
Abstract
Raman spectroscopy (RS) is an emerging analytical technique that can be used to develop and deploy precision agriculture. RS allows for confirmatory diagnostic of biotic and abiotic stresses on plants. Specifically, RS can be used for Huanglongbing (HLB) diagnostics on both orange and grapefruit trees, as well as detection and identification of various fungal and viral diseases. The questions that remain to be answered is how early can RS detect and identify the disease and whether RS is more sensitive than qPCR, the "golden standard" in pathogen diagnostics? Using RS and HLB as case study, we monitored healthy (qPCR-negative) in-field grown citrus trees and compared their spectra to the spectra collected from healthy orange and grapefruit trees grown in a greenhouse with restricted insect access and confirmed as HLB free by qPCR. Our result indicated that RS was capable of early prediction of HLB and that nearly all in-field qPCR-negative plants were infected by the disease. Using advanced multivariate statistical analysis, we also showed that qPCR-negative plants exhibited HLB-specific spectral characteristics that can be distinguished from unrelated nutrition deficit characteristics. These results demonstrate that RS is capable of much more sensitive diagnostics of HLB compared to qPCR.
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Affiliation(s)
- Lee Sanchez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843, United States
| | - Shankar Pant
- Texas A&M AgriLife Research and Extension Center at Weslaco, Texas, 78596, United States
- Agricultural Research Service, U.S. Department of Agriculture, Stillwater, OK, United States
| | - Kranthi Mandadi
- Texas A&M AgriLife Research and Extension Center at Weslaco, Texas, 78596, United States.
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, 77843, United States.
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843, United States.
- The Institute for Quantum Science and Engineering, Texas A&M University, College Station, Texas, 77843, United States.
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Keriö S, Terhonen E, LeBoldus JM. Safe DNA-extraction Protocol Suitable for Studying Tree-fungus Interactions. Bio Protoc 2020; 10:e3634. [PMID: 33659305 PMCID: PMC7920321 DOI: 10.21769/bioprotoc.3634] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/25/2020] [Accepted: 03/17/2020] [Indexed: 11/02/2022] Open
Abstract
We present a safe and low-cost method suitable for DNA extraction from mycelium and tree tissue samples. After sample preparation, the extraction takes about 60 min. Method performance was tested by extracting DNA from various tree tissue samples and from mycelium grown on solid and liquid media. DNA was extracted from juvenile and mature host material (Picea abies, Populus trichocarpa, Pseudotsuga menziesii) infected with different pathogens (Heterobasidion annosum, Heterobasidion parviporum, Leptographium wagenerii, Sphaerulina musiva). Additionally, DNA was extracted from pure cultures of the pathogens and several endophytic fungi. PCR success rate was 100% for young poplar material and fungal samples, and 48-72% for conifer and mature broadleaved plant samples. We recommend using 10-50 mg of fresh sample for the best results. The method offers a safe and low-cost DNA extraction alternative to study tree-fungus interactions, and is a potential resource for teaching purposes.
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Affiliation(s)
- Susanna Keriö
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis OR, 97331, USA
- Department of Forestry and Horticulture, Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven CT, 06511, USA
| | - Eeva Terhonen
- Department of Forest Botany and Tree Physiology, Büsgen Institute, Büsgenweg 2, 37077 Göttingen, Germany
| | - Jared M. LeBoldus
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis OR, 97331, USA
- Department of Forest Engineering, Resources and Management, Oregon State University, 210 Snell Hall, Corvallis OR, 97331, USA
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Fadiji AE, Babalola OO. Metagenomics methods for the study of plant-associated microbial communities: A review. J Microbiol Methods 2020; 170:105860. [PMID: 32027927 DOI: 10.1016/j.mimet.2020.105860] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 12/20/2022]
Abstract
Plant microbiota have different effects on the plant which can be beneficial or pathogenic. In this study, we concentrated on beneficial microbes associated with plants using endophytic microbes as a case study. Detailed knowledge of the microbial diversity, abundance, composition, functional genes patterns, and metabolic pathways at genome level could assist in understanding the contributions of microbial community towards plant growth and health. Recently, the study of microbial community has improved greatly with the discovery of next-generation sequencing and bioinformatics technologies. Analysis of next generation sequencing data and a proper computational method plays a key role in examining microbial metagenome. This review presents the general metagenomics and computational methods used in processing plant associated metagenomes with concentration on endophytes. This includes 1) introduction of plant-associated microbiota and the factors driving their diversity. 2) plant metagenome focusing on DNA extraction, verification and quality control. 3) metagenomics methods used in community analysis of endophytes focusing on maize plant and, 4) computational methods used in the study of endophytic microbiomes. Limitations and future prospects of metagenomics and computational methods for the analysis of plant-associated metagenome (endophytic metagenome) were also discussed with the aim of fostering its development. We conclude that there is need to adopt advanced genomic features such as k-mers of random size, which do not depend on annotation and can represent other sequence alternatives.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa.
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Marengo A, Cagliero C, Sgorbini B, Anderson JL, Emaus MN, Bicchi C, Bertea CM, Rubiolo P. Development of an innovative and sustainable one-step method for rapid plant DNA isolation for targeted PCR using magnetic ionic liquids. PLANT METHODS 2019; 15:23. [PMID: 30899320 PMCID: PMC6408755 DOI: 10.1186/s13007-019-0408-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/02/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bottleneck in the bioanalytical workflow. New opportunities have been created by the use of magnetic ionic liquids (MILs) thanks to their affinity for nucleic acids. RESULTS In the present study, a MIL-based magnet-assisted dispersive liquid-liquid microextraction (maDLLME) method was optimized for the extraction of genomic DNA from Arabidopsis thaliana (L.) Heynh leaves. MILs containing different metal centers were tested and the extraction method was optimized in terms of MIL volume and extraction time for purified DNA and crude lysates. The proposed approach yielded good extraction efficiency and is compatible with both quantitative analysis through fluorimetric-based detection and qualitative analysis as PCR amplification of multi and single locus genes. The protocol was successfully applied to a set of plant species and tissues. CONCLUSIONS The developed MIL-based maDLLME approach exhibits good enrichment of nucleic acids for extraction of template suitable for targeted PCR; it is very fast, sustainable and potentially automatable thereby representing a powerful tool for screening plants rapidly using DNA-based methods.
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Affiliation(s)
- Arianna Marengo
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
| | - Cecilia Cagliero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
| | - Barbara Sgorbini
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
| | | | - Miranda N. Emaus
- Department of Chemistry, Iowa State University, Ames, IA 50011 USA
| | - Carlo Bicchi
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
| | - Cinzia M. Bertea
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Unità di Fisiologia Vegetale, Università di Torino, via Quarello 15/A, 10135 Turin, Italy
| | - Patrizia Rubiolo
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
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