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Valarmathi R, Mahadeva Swamy HK, Appunu C, Suresha GS, Mohanraj K, Hemaprabha G, Mahadevaiah C, Ulaganathan V. Comparative transcriptome profiling to unravel the key molecular signalling pathways and drought adaptive plasticity in shoot borne root system of sugarcane. Sci Rep 2023; 13:12853. [PMID: 37553413 PMCID: PMC10409851 DOI: 10.1038/s41598-023-39970-1] [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: 04/19/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Sugarcane root system comprises of superficial sett roots as well as deeply-penetrating shoot borne roots (SBR) with latter being the permanent root system. In sugarcane, the healthy SBR contributes to a better crop yield and it also helps to produce multiple ratoon crops after the harvest. There is a dearth of in-depth knowledge on SBR system architecture and its functional role in modern day commercial hybrids. A comprehensive phenotypic, anatomical and whole transcriptome profiling, conducted between the commercial sugarcane hybrids and a wild germplasm Erianthus, found a developmental delay in both initiation and establishment of the SBR in commercial hybrid compared to Erianthus. The SBR system in Erianthus proved to be an extensive drought-adaptive root system architecture that significantly contributes to drought tolerance. On the other hand, SBRs in the commercial hybrids showed an irreversible collapse and damage of the root cells under drought stress. The outcomes from the comparative analysis of the transcriptome data showed a significant upregulation of the genes that regulate important stress signalling pathways viz., sugar, calcium, hormone signalling and phenylpropanoid biosynthesis in the SBRs of Erianthus. It was found that through these key signalling pathways, Erianthus SBRs triggered the downstream signalling cascade to impart physiological responses like osmoprotection, modification of the cell walls, detoxification of reactive oxygen species, expression of drought responsive transcription factors, maintenance of cell stability and lateral root development. The current study forms a basis for further exploration of the Shoot Borne Root system as a valuable breeding target to develop drought tolerant sugarcane genotypes.
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Affiliation(s)
- R Valarmathi
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India.
| | - H K Mahadeva Swamy
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - C Appunu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - G S Suresha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - K Mohanraj
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - G Hemaprabha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - C Mahadevaiah
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - V Ulaganathan
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
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Li N, Zhang Y, Wang X, Ma H, Sun Y, Li G, Zhang S. Integration of Transcriptomic and Proteomic Profiles Reveals Multiple Levels of Genetic Regulation of Taproot Growth in Sugar Beet ( Beta vulgaris L.). FRONTIERS IN PLANT SCIENCE 2022; 13:882753. [PMID: 35909753 PMCID: PMC9326478 DOI: 10.3389/fpls.2022.882753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Sugar beet taproot growth and development is a complex biological process involving morphogenesis and dry matter accumulation. However, the molecular regulatory mechanisms underlying taproot growth and development remain elusive. We performed a correlation analysis of the proteome and transcriptome in two cultivars (SD13829 and BS02) at the start and the highest points of the taproot growth rate. The corresponding correlation coefficients were 0.6189, 0.7714, 0.6803, and 0.7056 in four comparison groups. A total of 621 genes were regulated at both transcriptional and translational levels, including 190, 71, 140, and 220 in the BS59-VS-BS82, BS59-VS-SD59, BS82-VS-SD82, and SD59-VS-SD82 groups, respectively. Ten, 32, and 68 correlated-DEGs-DEPs (cor-DEGs-DEPs) were significantly enrdiched in the proteome and transcriptome of the BS59-VS-BS82, SD59-VS-SD82, and BS82-VS-SD82 groups, respectively, which included ribonuclease 1-like protein, DEAD-box ATP-dependent RNA helicase, TolB protein, heat shock protein 83, 20 kDa chaperonin, polygalacturonase, endochitinase, brassinolide and gibberellin receptors (BRI1 and GID1), and xyloglucan endotransglucosylase/hydrolase (XTH). In addition, Beta vulgaris XTH could enhance the growth and development of Arabidopsis primary roots by improving cell growth in the root tip elongation zone. These findings suggested that taproot growth and expansion might be regulated at transcriptional and posttranscriptional levels and also may be attributed to cell wall metabolism to improve cell wall loosening and elongation.
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G. Viana W, Scharwies JD, Dinneny JR. Deconstructing the root system of grasses through an exploration of development, anatomy and function. PLANT, CELL & ENVIRONMENT 2022; 45:602-619. [PMID: 35092025 PMCID: PMC9303260 DOI: 10.1111/pce.14270] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 05/16/2023]
Abstract
Well-adapted root systems allow plants to grow under resource-limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below-ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts-list of elements that function together in an integrated root system to promote survival and crop productivity.
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Affiliation(s)
| | | | - José R. Dinneny
- Department of BiologyStanford UniversityStanfordCaliforniaUSA
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Liu T, Zhang X. Comparative transcriptome and metabolome analysis reveal glutathione metabolic network and functional genes underlying blue and red-light mediation in maize seedling leaf. BMC PLANT BIOLOGY 2021; 21:593. [PMID: 34906076 PMCID: PMC8670197 DOI: 10.1186/s12870-021-03376-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Light quality severely affects biosynthesis and metabolism-associated process of glutathione. However, the role of specific light is still unclear on the glutathione metabolism. In this article, comparatively transcriptome and metabolome methods are used to fully understand the blue and red-light conditions working on the glutathione metabolism in maize seedling leaf. RESULTS There are 20 differently expressed genes and 4 differently expressed metabolites in KEGG pathway of glutathione metabolism. Among them, 12 genes belong to the glutathione S-transferase family, 3 genes belong to the ascorbate peroxidase gene family and 2 genes belong to the ribonucleoside-diphosphate reductase gene family. Three genes, G6PD, SPDS1, and GPX1 belong to the gene family of glucose 6-phosphate dehydrogenase, spermidine synthase, and glutathione peroxidase, respectively. Four differently expressed metabolites are identified. Three of them, Glutathione disulfide, Glutathione, and l-γ-Glutamyl-L-amino acid are decreased while L-Glutamate is increased. In addition, Through PPI analysis, two annotated genes gst16 and DAAT, and 3 unidentified genes 100381533, pco105094 and umc2770, identified as RPP13-like3, BCAT-like1and GMPS, were obtained. By the analysis of protein sequence and PPI network, we predict that pco105094 and umc2770 were involved in the GSSG-GSH and AsA-GSH cycle in the network of glutathione metabolism. CONCLUSIONS Compared to red light, blue light remarkably changed the transcription signal transduction and metabolism of glutathione metabolism. Differently expressed genes and metabolic mapped to the glutathione metabolism signaling pathways. In total, we obtained three unidentified genes, and two of them were predicted in current glutathione metabolism network. This result will contribute to the research of glutathione metabolism of maize.
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Affiliation(s)
- Tiedong Liu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xiwen Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
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Adaptive Agricultural Strategies for Facing Water Deficit in Sweet Maize Production: A Case Study of a Semi-Arid Mediterranean Region. WATER 2021. [DOI: 10.3390/w13223285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Maize is a crucial global commodity, which is used not only for food, but also as an alternative crop in biogas production and as a major energy-supply ingredient in animal diets. However, climate change is jeopardizing current maize production due to its direct impact on weather instability and water availability or its indirect effects on regional climate suitability loss. Hence, new areas for sweet maize cultivation should be considered in the future. Therefore, this study focuses on the possibility of producing maize in a challenging environment in Southern Italy considering rainfed cultivation and two irrigation regimes (full and deficit). The experiment was conducted during two subsequent growing seasons under semi-arid Mediterranean climate conditions. The overall results indicated a significant difference in biomass and yield between irrigated and non-irrigated treatments, and between full and deficit irrigation. Sweet maize cultivated under deficit irrigation gained less biomass than under full irrigation and its development and fruit maturation were delayed. Under deficit irrigation, the plants gave lower yields and a higher percentage of the panicle weight consisted of kernels. Irrigation water productivity was higher for deficit than for full irrigated treatment. These findings indicate the feasibility of sweet maize production in semi-arid areas of Southern Italy using adaptive agricultural strategies including deficit irrigation and controlled water stress. Given the importance of maize production, understanding of maize growth and productivity in a challenging environment may support future agricultural programming and thereby contribute e to mitigation of the direct and indirect effects of climate change.
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Sheoran S, Kumar S, Kumar P, Meena RS, Rakshit S. Nitrogen fixation in maize: breeding opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1263-1280. [PMID: 33677701 DOI: 10.1007/s00122-021-03791-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
Maize (Zea mays L.) is a highly versatile crop with huge demand of nitrogen (N) for its growth and development. N is the most essential macronutrient for crop production. Despite being the highest abundant element in the atmosphere (~ 78%), it is scarcely available for plant growth. To fulfil the N demand, commercial agriculture is largely dependent on synthetic fertilizers. Excessive dependence on inorganic fertilizers has created extensive ecological as well as economic problems worldwide. Hence, for a sustainable solution to nitrogenous fertilizer use, development of biological nitrogen fixation (BNF) in cereals will be the best alternative. BNF is a well-known mechanism in legumes where diazotrophs convert atmospheric nitrogen (N≡N) to plant-available form, ammonium (NH4+). From many decades, researchers have dreamt to develop a similar symbiotic partnership as in legumes to the cereal crops. A large number of endophytic diazotrophs have been found associated with maize. Elucidation of the genetic and molecular aspects of their interaction will open up new avenues to introgress BNF in maize breeding. With the advanced understanding of N-fixation process, researchers are at a juncture of breeding and engineering this symbiotic relationships in cereals. Different breeding, genetic engineering, omics, gene editing, and synthetic biology approaches will be discussed in this review to make BNF a reality in cereals. It will help to provide a road map to develop/improve the BNF in maize to an advance step for the sustainable production system to achieve the food and nutritional security.
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Affiliation(s)
- Seema Sheoran
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 1410 04, India
| | - Sandeep Kumar
- ICAR-Indian Institute of Pulses Research, Regional Station, Phanda, Bhopal, 462 030, India
| | - Pradeep Kumar
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 1410 04, India
| | - Ram Swaroop Meena
- Department of Agronomy, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221 005, India
| | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 1410 04, India.
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Xu L, Sun X, Wan X, Li H, Yan F, Han R, Li H, Li Z, Tian Y, Liu X, Kang X, Wang Y. Identification of a Bacillus amyloliquefaciens H6 Thioesterase Involved in Zearalenone Detoxification by Transcriptomic Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10071-10080. [PMID: 32815728 DOI: 10.1021/acs.jafc.0c03954] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Zearalenone (ZEA), a nonsteroidal estrogenic mycotoxin produced by Fusarium graminearum, induces hyperestrogenic responses in mammals and can cause reproductive disorders in farm animals. In this study, a transcriptome analysis of Bacillus amyloliquefaciens H6, which was previously identified as a ZEA-degrading bacterium, was conducted with high-throughput sequencing technology, and the differentially expressed genes were subjected to gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses. Among the 16 upregulated genes, BAMF_RS30125 was predicted to be the key gene responsible for ZEA degradation. The protein encoded by BAMF_RS30125 was then expressed in Escherichia coli, and this recombinant protein (named ZTE138) significantly reduced the ZEA content, as determined by the enzyme-linked immunosorbent assay (ELISA) and high-performance liquid chromatography (HPLC), and decreased the proliferating activity of ZEA in MCF-7 cells. What is more, the liquid chromatography-tandem mass spectrometry (LC-MS/MS) results showed that the relative molecular mass and the structure of ZEA also changed. Sequence alignment of the ZTE138 protein showed that it is a protease that belongs to the YBGC/FADM family of coenzyme A thioesterases, and thus, the protein can presumably cleave the ZEA lactone bond and break down its macrolide ring.
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Affiliation(s)
- Laipeng Xu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
| | - Xiangli Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
| | - Xianhua Wan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
| | - Hui Li
- College of Environmental and Resource Sciences, Henan Agricultural University, Zhengzhou 450000, China
| | - Fengbin Yan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Hong Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
| | - Yanbin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450000, China
- Henan Research Center of Germplasm Resources for Poultry, Zhengzhou 450002, China
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8
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Current Progress in Nitrogen Fixing Plants and Microbiome Research. PLANTS 2020; 9:plants9010097. [PMID: 31940996 PMCID: PMC7020401 DOI: 10.3390/plants9010097] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/02/2020] [Accepted: 01/08/2020] [Indexed: 01/10/2023]
Abstract
In agroecosystems, nitrogen is one of the major nutrients limiting plant growth. To meet the increased nitrogen demand in agriculture, synthetic fertilizers have been used extensively in the latter part of the twentieth century, which have led to environmental challenges such as nitrate pollution. Biological nitrogen fixation (BNF) in plants is an essential mechanism for sustainable agricultural production and healthy ecosystem functioning. BNF by legumes and associative, endosymbiotic, and endophytic nitrogen fixation in non-legumes play major roles in reducing the use of synthetic nitrogen fertilizer in agriculture, increased plant nutrient content, and soil health reclamation. This review discusses the process of nitrogen-fixation in plants, nodule formation, the genes involved in plant-rhizobia interaction, and nitrogen-fixing legume and non-legume plants. This review also elaborates on current research efforts involved in transferring nitrogen-fixing mechanisms from legumes to non-legumes, especially to economically important crops such as rice, maize, and wheat at the molecular level and relevant other techniques involving the manipulation of soil microbiome for plant benefits in the non-legume root environment.
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Li J, Chen F, Li Y, Li P, Wang Y, Mi G, Yuan L. ZmRAP2.7, an AP2 Transcription Factor, Is Involved in Maize Brace Roots Development. FRONTIERS IN PLANT SCIENCE 2019; 10:820. [PMID: 31333689 PMCID: PMC6621205 DOI: 10.3389/fpls.2019.00820] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/06/2019] [Indexed: 05/12/2023]
Abstract
In maize, shoot-borne roots dominate the whole root system and play essential roles in water and nutrient acquisition and lodging tolerance. Shoot-borne roots initiate at shoot nodes, including crown roots from the belowground nodes and brace roots from aboveground nodes. In contrast to crown roots, few genes for brace roots development have been identified. Here, we characterized a maize AP2/ERF transcription factor, ZmRAP2.7, to be involved in brace roots development. ZmRAP2.7 expressed in all types of roots, and the encoded protein localized in the nucleus with transcriptional activation activity. A maize transposon insert mutant RAP2.7-Mu defective in ZmRAP2.7 expression revealed a decreased number of brace roots but not crown roots. Maize Corngrass1 mutant, which showed an elevated expression of ZmRAP2.7, however, revealed an increased number of brace roots. The ZmRAP2.7-based association analysis in a maize panel further identified a SNP marker at the fifth exon of gene to be associated with number of brace roots. These results uncovered a function of ZmRAP2.7 in brace roots development and provided the valuable gene and allele for genetic improvement of maize root systems.
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Affiliation(s)
- Jieping Li
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Plant Science, School of Life Sciences, Henan University, Kaifeng, China
| | - Fanjun Chen
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Yanqing Li
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Pengcheng Li
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics, Co-Innovation Center for Modern Production Technology of Grain Crops, MOE, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Yuanqing Wang
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guohua Mi
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Lixing Yuan
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
- *Correspondence: Lixing Yuan,
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Van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, Lopez J, Weimer BC, Eisen JA, Shapiro HY, Ané JM, Bennett AB. Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLoS Biol 2018; 16:e2006352. [PMID: 30086128 PMCID: PMC6080747 DOI: 10.1371/journal.pbio.2006352] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/03/2018] [Indexed: 12/19/2022] Open
Abstract
Plants are associated with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals, including maize. We studied an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe region of Oaxaca, Mexico. This landrace is characterized by the extensive development of aerial roots that secrete a carbohydrate-rich mucilage. Analysis of the mucilage microbiota indicated that it was enriched in taxa for which many known species are diazotrophic, was enriched for homologs of genes encoding nitrogenase subunits, and harbored active nitrogenase activity as assessed by acetylene reduction and 15N2 incorporation assays. Field experiments in Sierra Mixe using 15N natural abundance or 15N-enrichment assessments over 5 years indicated that atmospheric nitrogen fixation contributed 29%–82% of the nitrogen nutrition of Sierra Mixe maize. Nitrogen is an essential nutrient for plants, and for many nonlegume crops, the requirement for nitrogen is primarily met by the use of inorganic fertilizers. These fertilizers are produced from fossil fuel by energy-intensive processes that are estimated to use 1% to 2% of the total global energy supply and produce an equivalent share of greenhouse gases. Because maize (Zea mays L.) is a significant recipient of nitrogen fertilization, a research goal for decades has been to identify or engineer mechanisms for biological fixation of atmospheric nitrogen in association with this crop. We hypothesized that isolated indigenous landraces of maize grown using traditional practices with little or no fertilizer might have evolved strategies to improve plant performance under low-nitrogen nutrient conditions. Here, we show that for one such maize landrace grown in nitrogen-depleted fields near Oaxaca, Mexico, 29%–82% of the plant nitrogen is derived from atmospheric nitrogen. High levels of nitrogen fixation are supported, at least in part, by the abundant production of a sugar-rich mucilage associated with aerial roots that provides a home to a complex nitrogen-fixing microbiome.
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Affiliation(s)
- Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Pablo Zamora
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Pierre-Marc Delaux
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Cristobal Heitmann
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Dhileepkumar Jayaraman
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Shanmugam Rajasekar
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Danielle Graham
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Junko Maeda
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Donald Gibson
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Kevin D. Schwartz
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Alison M. Berry
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Srijak Bhatnagar
- Genome Center, University of California, Davis, California, United States of America
| | - Guillaume Jospin
- Genome Center, University of California, Davis, California, United States of America
| | - Aaron Darling
- Genome Center, University of California, Davis, California, United States of America
| | - Richard Jeannotte
- Department of Population Health and Reproduction, University of California, Davis, California, United States of America
| | - Javier Lopez
- Instituto Tecnológico del Valle de Oaxaca, Oaxaca, Mexico
| | - Bart C. Weimer
- Department of Population Health and Reproduction, University of California, Davis, California, United States of America
| | - Jonathan A. Eisen
- Genome Center, University of California, Davis, California, United States of America
| | - Howard-Yana Shapiro
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Mars, Incorporated, McLean, Virginia, United States of America
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Alan B. Bennett
- Department of Plant Sciences, University of California, Davis, California, United States of America
- * E-mail:
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11
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Kong X, Liu D, Liao X, Zheng J, Diao Y, Liu Y, Zhou R. Comparative Analysis of the Cytology and Transcriptomes of the Cytoplasmic Male Sterility Line H276A and Its Maintainer Line H276B of Cotton (Gossypium barbadense L.). Int J Mol Sci 2017; 18:ijms18112240. [PMID: 29068396 PMCID: PMC5713210 DOI: 10.3390/ijms18112240] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 10/05/2017] [Accepted: 10/19/2017] [Indexed: 12/12/2022] Open
Abstract
In this study, the tetrad stage of microspore development in a new cotton (Gossypium barbadense L.) cytoplasmic male sterility (CMS) line, H276A, was identified using paraffin sections at the abortion stage. To explore the molecular mechanism underlying CMS in cotton, a comparative transcriptome analysis between the CMS line H276A and its maintainer line H276B at the tetrad stage was conducted using an Illumina HiSeq 4000 platform. The comparison of H276A with H276B revealed a total of 64,675 genes, which consisted of 59,255 known and 5420 novel genes. An analysis of the two libraries with a given threshold yielded a total of 3603 differentially expressed genes (DEGs), which included 1363 up- and 2240 down-regulated genes. Gene Ontology (GO) annotation showed that 2171 DEGs were distributed into 38 categories, and a Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that 2683 DEGs were classified into 127 groups. Thirteen DEGs were randomly selected and detected by quantitative reverse-transcribed PCR (qRT-PCR), and the results indicated that the transcriptome sequencing results were reliable. The bioinformatic analysis results in conjunction with previously reported data revealed key DEGs that might be associated with the male sterility features of H276A. Our results provide a comprehensive foundation for understanding anther development and will accelerate the study of the molecular mechanisms of CMS in cotton.
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Affiliation(s)
- Xiangjun Kong
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China.
| | - Dongmei Liu
- Key Laboratory of Plant-Microbe Interactions, Department of Life Science and Food, Shangqiu Normal University, Shangqiu 476000, China.
| | - Xiaofang Liao
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China.
| | - Jie Zheng
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China.
| | - Yong Diao
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China.
| | - Yiding Liu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China.
| | - Ruiyang Zhou
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China.
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Khan S, Upadhyay S, Khan F, Tandon S, Shukla RK, Ghosh S, Gupta V, Banerjee S, Ur Rahman L. Comparative transcriptome analysis reveals candidate genes for the biosynthesis of natural insecticide in Tanacetum cinerariifolium. BMC Genomics 2017; 18:54. [PMID: 28068903 PMCID: PMC5220608 DOI: 10.1186/s12864-016-3409-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/10/2016] [Indexed: 11/26/2022] Open
Abstract
Background Pyrethrins are monoterpenoids and consist of either a chrysanthemic acid or pyrethric acid with a rethrolone moiety. Natural pyrethrins are safe and eco-friendly while possessing strong insecticidal properties. Despite such advantages of commercial value coming with the eco-friendly tag, most enzymes/genes involved in the pyrethrin biosynthesis pathway remain unidentified and uncharacterized. Since the flowers of Tanacetum cinerariifolium are rich in major pyrethrins, next generation transcriptome sequencing was undertaken to compare the flowers and the leaves of the plant de novo to identify differentially expressed transcripts and ascertain which among them might be involved in and responsible for the differential accumulation of pyrethrins in T. cinerariifolium flowers. Results In this first tissue specific transcriptome analysis of the non-model plant T. cinerariifolium, a total of 23,200,000 and 28,500,110 high quality Illumina next generation sequence reads, with a length of 101 bp, were generated for the flower and leaf tissue respectively. After functional enrichment analysis and GO based annotation using public protein databases such as UniRef, PFAM, SMART, KEGG and NR, 4443 and 8901 unigenes were identified in the flower and leaf tissue respectively. These could be assigned to 13344 KEGG pathways and the pyrethrin biosynthesis contextualized. The 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway was involved in the biosynthesis of acid moiety of pyrethrin and this pathway predominated in the flowers as compared to the leaves. However, enzymes related to oxylipin biosynthesis were found predominantly in the leaf tissue, which suggested that major steps of pyrethrin biosynthesis occurred in the flowers. Conclusions Transcriptome comparison between the flower and leaf tissue of T. cinerariifolium provided an elaborate list of tissue specific transcripts that was useful in elucidating the differences in the expression of the biosynthetic pathways leading to differential presence of pyrethrin in the flowers. The information generated on genes, pathways and markers related to pyrethrin biosynthesis in this study will be helpful in enhancing the production of these useful compounds for value added breeding programs. Related proteome comparison to overlay our transcriptome comparison can generate more relevant information to better understand flower specific accumulation of secondary metabolites in general and pyrethrin accumulation in particular. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3409-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sana Khan
- Plant Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Swati Upadhyay
- Plant Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Feroz Khan
- Metabolic and Structural Biology Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Sudeep Tandon
- Process Chemistry and Chemical Engineering Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Rakesh Kumar Shukla
- Plant Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Sumit Ghosh
- Plant Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Vikrant Gupta
- Plant Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Suchitra Banerjee
- Plant Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Laiq Ur Rahman
- Plant Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India.
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Yu R, Wang J, Xu L, Wang Y, Wang R, Zhu X, Sun X, Luo X, Xie Y, Everlyne M, Liu L. Transcriptome Profiling of Taproot Reveals Complex Regulatory Networks during Taproot Thickening in Radish (Raphanus sativus L.). FRONTIERS IN PLANT SCIENCE 2016; 7:1210. [PMID: 27597853 PMCID: PMC4992731 DOI: 10.3389/fpls.2016.01210] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 07/29/2016] [Indexed: 05/19/2023]
Abstract
Radish (Raphanus sativus L.) is one of the most important vegetable crops worldwide. Taproot thickening represents a critical developmental period that determines yield and quality in radish life cycle. To isolate differentially expressed genes (DGEs) involved in radish taproot thickening process and explore the molecular mechanism underlying taproot development, three cDNA libraries from radish taproot collected at pre-cortex splitting stage (L1), cortex splitting stage (L2), and expanding stage (L3) were constructed and sequenced by RNA-Seq technology. More than seven million clean reads were obtained from the three libraries, from which 4,717,617 (L1, 65.35%), 4,809,588 (L2, 68.24%) and 4,973,745 (L3, 69.45%) reads were matched to the radish reference genes, respectively. A total of 85,939 transcripts were generated from three libraries, from which 10,450, 12,325, and 7392 differentially expressed transcripts (DETs) were detected in L1 vs. L2, L1 vs. L3, and L2 vs. L3 comparisons, respectively. Gene Ontology and pathway analysis showed that many DEGs, including EXPA9, Cyclin, CaM, Syntaxin, MADS-box, SAUR, and CalS were involved in cell events, cell wall modification, regulation of plant hormone levels, signal transduction and metabolisms, which may relate to taproot thickening. Furthermore, the integrated analysis of mRNA-miRNA revealed that 43 miRNAs and 92 genes formed 114 miRNA-target mRNA pairs were co-expressed, and three miRNA-target regulatory networks of taproot were constructed from different libraries. Finally, the expression patterns of 16 selected genes were confirmed using RT-qPCR analysis. A hypothetical model of genetic regulatory network associated with taproot thickening in radish was put forward. The taproot formation of radish is mainly attributed to cell differentiation, division and expansion, which are regulated and promoted by certain specific signal transduction pathways and metabolism processes. These results could provide new insights into the complex molecular mechanism underlying taproot thickening and facilitate genetic improvement of taproot in radish.
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Affiliation(s)
- Rugang Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- School of Life Science, Huaibei Normal UniversityHuaibei, China
| | - Jing Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Ronghua Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - Xiaochuan Sun
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yang Xie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Muleke Everlyne
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
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14
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Wang S, Wang C, Zhang XX, Chen X, Liu JJ, Jia XF, Jia SQ. Transcriptome de novo assembly and analysis of differentially expressed genes related to cytoplasmic male sterility in cabbage. PLANT PHYSIOLOGY AND BIOCHEMISTRY 2016; 105:224-232. [PMID: 0 DOI: 10.1016/j.plaphy.2016.04.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 05/19/2023]
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15
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Zaidi PH, Rashid Z, Vinayan MT, Almeida GD, Phagna RK, Babu R. QTL mapping of agronomic waterlogging tolerance using recombinant inbred lines derived from tropical maize (Zea mays L) germplasm. PLoS One 2015; 10:e0124350. [PMID: 25884393 PMCID: PMC4401703 DOI: 10.1371/journal.pone.0124350] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 03/09/2015] [Indexed: 11/18/2022] Open
Abstract
Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate rapid introgression of waterlogging tolerance in tropical maize breeding programs.
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Affiliation(s)
- Pervez Haider Zaidi
- International Maize and Wheat Improvement Center (CIMMYT)—Asia, C/o International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Zerka Rashid
- International Maize and Wheat Improvement Center (CIMMYT)—Asia, C/o International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Madhumal Thayil Vinayan
- International Maize and Wheat Improvement Center (CIMMYT)—Asia, C/o International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | | | | | - Raman Babu
- International Maize and Wheat Improvement Center (CIMMYT)—Asia, C/o International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- * E-mail:
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Rogers ED, Benfey PN. Regulation of plant root system architecture: implications for crop advancement. Curr Opin Biotechnol 2014; 32:93-98. [PMID: 25448235 DOI: 10.1016/j.copbio.2014.11.015] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 11/13/2014] [Indexed: 11/15/2022]
Abstract
Root system architecture (RSA) plays a major role in plant fitness, crop performance, and grain yield yet only recently has this role been appreciated. RSA describes the spatial arrangement of root tissue within the soil and is therefore crucial to nutrient and water uptake. Recent studies have identified many of the genetic and environmental factors influencing root growth that contribute to RSA. Some of the identified genes have the potential to limit crop loss caused by environmental extremes and are currently being used to confer drought tolerance. It is hypothesized that manipulating these and other genes that influence RSA will be pivotal for future crop advancements worldwide.
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Affiliation(s)
- Eric D Rogers
- Department of Biology and Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA
| | - Philip N Benfey
- Department of Biology and Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA.
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17
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Transcriptome-wide identification of the genes responding to replanting disease in Rehmannia glutinosa L. roots. Mol Biol Rep 2014; 42:881-92. [DOI: 10.1007/s11033-014-3825-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 11/10/2014] [Indexed: 01/22/2023]
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18
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Atkinson JA, Rasmussen A, Traini R, Voß U, Sturrock C, Mooney SJ, Wells DM, Bennett MJ. Branching out in roots: uncovering form, function, and regulation. PLANT PHYSIOLOGY 2014; 166:538-50. [PMID: 25136060 PMCID: PMC4213086 DOI: 10.1104/pp.114.245423] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/12/2013] [Indexed: 05/18/2023]
Abstract
Root branching is critical for plants to secure anchorage and ensure the supply of water, minerals, and nutrients. To date, research on root branching has focused on lateral root development in young seedlings. However, many other programs of postembryonic root organogenesis exist in angiosperms. In cereal crops, the majority of the mature root system is composed of several classes of adventitious roots that include crown roots and brace roots. In this Update, we initially describe the diversity of postembryonic root forms. Next, we review recent advances in our understanding of the genes, signals, and mechanisms regulating lateral root and adventitious root branching in the plant models Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa). While many common signals, regulatory components, and mechanisms have been identified that control the initiation, morphogenesis, and emergence of new lateral and adventitious root organs, much more remains to be done. We conclude by discussing the challenges and opportunities facing root branching research.
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Affiliation(s)
- Jonathan A Atkinson
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (J.A.A., A.R., R.T., U.V., C.S., S.J.M., D.M.W., M.J.B.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (M.J.B.)
| | - Amanda Rasmussen
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (J.A.A., A.R., R.T., U.V., C.S., S.J.M., D.M.W., M.J.B.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (M.J.B.)
| | - Richard Traini
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (J.A.A., A.R., R.T., U.V., C.S., S.J.M., D.M.W., M.J.B.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (M.J.B.)
| | - Ute Voß
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (J.A.A., A.R., R.T., U.V., C.S., S.J.M., D.M.W., M.J.B.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (M.J.B.)
| | - Craig Sturrock
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (J.A.A., A.R., R.T., U.V., C.S., S.J.M., D.M.W., M.J.B.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (M.J.B.)
| | - Sacha J Mooney
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (J.A.A., A.R., R.T., U.V., C.S., S.J.M., D.M.W., M.J.B.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (M.J.B.)
| | - Darren M Wells
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (J.A.A., A.R., R.T., U.V., C.S., S.J.M., D.M.W., M.J.B.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (M.J.B.)
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (J.A.A., A.R., R.T., U.V., C.S., S.J.M., D.M.W., M.J.B.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (M.J.B.)
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Zhang Y, Paschold A, Marcon C, Liu S, Tai H, Nestler J, Yeh CT, Opitz N, Lanz C, Schnable PS, Hochholdinger F. The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4919-30. [PMID: 24928984 PMCID: PMC4144770 DOI: 10.1093/jxb/eru249] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The maize (Zea mays L.) Aux/IAA protein RUM1 (ROOTLESS WITH UNDETECTABLE MERISTEMS 1) controls seminal and lateral root initiation. To identify RUM1-dependent gene expression patterns, RNA-Seq of the differentiation zone of primary roots of rum1 mutants and the wild type was performed in four biological replicates. In total, 2 801 high-confidence maize genes displayed differential gene expression with Fc ≥2 and FDR ≤1%. The auxin signalling-related genes rum1, like-auxin1 (lax1), lax2, (nam ataf cuc 1 nac1), the plethora genes plt1 (plethora 1), bbm1 (baby boom 1), and hscf1 (heat shock complementing factor 1) and the auxin response factors arf8 and arf37 were down-regulated in the mutant rum1. All of these genes except nac1 were auxin-inducible. The maize arf8 and arf37 genes are orthologues of Arabidopsis MP/ARF5 (MONOPTEROS/ARF5), which controls the differentiation of vascular cells. Histological analyses of mutant rum1 roots revealed defects in xylem organization and the differentiation of pith cells around the xylem. Moreover, histochemical staining of enlarged pith cells surrounding late metaxylem elements demonstrated that their thickened cell walls displayed excessive lignin deposition. In line with this phenotype, rum1-dependent mis-expression of several lignin biosynthesis genes was observed. In summary, RNA-Seq of RUM1-dependent gene expression in maize primary roots, in combination with histological and histochemical analyses, revealed the specific regulation of auxin signal transduction components by RUM1 and novel functions of RUM1 in vascular development.
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Affiliation(s)
- Yanxiang Zhang
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
| | - Anja Paschold
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
| | - Caroline Marcon
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University, Ames 50011-3650, Iowa, USA
| | - Huanhuan Tai
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
| | - Josefine Nestler
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
| | - Cheng-Ting Yeh
- Center for Plant Genomics, Iowa State University, Ames 50011-3650, Iowa, USA
| | - Nina Opitz
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max-Planck-Institute for Developmental Biology, 72076 Tuebingen, Germany
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames 50011-3650, Iowa, USA Center for Plant Genomics, Iowa State University, Ames 50011-3650, Iowa, USA
| | - Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
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Upadhyay S, Phukan UJ, Mishra S, Shukla RK. De novo leaf and root transcriptome analysis identified novel genes involved in steroidal sapogenin biosynthesis in Asparagus racemosus. BMC Genomics 2014; 15:746. [PMID: 25174837 PMCID: PMC4162912 DOI: 10.1186/1471-2164-15-746] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/21/2014] [Indexed: 01/01/2023] Open
Abstract
Background Saponins are mainly amphipathic glycosides that posses many biological activities and confer potential health benefits to humans. Inspite of its medicinal attributes most of the triterpenes and enzymes involved in the saponin biosynthesis remains uncharacterized at the molecular level. Since the major steroidal components are present in the roots of A. racemosus our study is focussed on the comparative denovo transcriptome analysis of root versus leaf tissue and identifying some root specific transcripts involved in saponin biosynthesis using high-throughput next generation transcriptome sequencing. Results After sequencing, de novo assembly and quantitative assessment, 126861 unigenes were finally generated with an average length of 1200 bp. Then functional annotation and GO enrichment analysis was performed by aligning all-unigenes with public protein databases including NR, SwissProt, and KEGG. Differentially expressed genes in root were initially identified using the RPKM method using digital subtraction between root and leaf. Twenty seven putative secondary metabolite related transcripts were experimentally validated for their expression in root or leaf tissue using q-RT PCR analysis. Most of the above selected transcripts showed preferential expression in root as compared to leaf supporting the digitally subtracted result obtained. The methyl jasmonate application induces the secondary metabolite related gene transcripts leading to their increased accumulation in plants. Therefore, the identified transcripts related to saponin biosynthesis were further analyzed for their induced expression after 3, 5 and 12 hours of exogenous application of Methyl Jasmonate in tissue specific manner. Conclusions In this study, we have identified a large set of cDNA unigenes from A. racemosus leaf and root tissue. This is the first transcriptome sequencing of this non-model species using Illumina, a next generation sequencing technology. The present study has also identified number of root specific transcripts showing homology with saponin biosynthetic pathway. An integrated pathway of identified saponin biosynthesis transcripts their tissue specific expression and induced accumulation after methyl jasmonate treatment was discussed. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-746) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Rakesh Kumar Shukla
- Biotechnology Division, Central Institute of Medicinal and Aromatic Plants, P,O, CIMAP, Near Kukrail Picnic Spot, Lucknow, U,P, India.
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Villordon AQ, Ginzberg I, Firon N. Root architecture and root and tuber crop productivity. TRENDS IN PLANT SCIENCE 2014; 19:419-25. [PMID: 24630073 DOI: 10.1016/j.tplants.2014.02.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/27/2014] [Accepted: 02/06/2014] [Indexed: 05/03/2023]
Abstract
It is becoming increasingly evident that optimization of root architecture for resource capture is vital for enabling the next green revolution. Although cereals provide half of the calories consumed by humans, root and tuber crops are the second major source of carbohydrates globally. Yet, knowledge of root architecture in root and tuber species is limited. In this opinion article, we highlight what is known about the root system in root and tuber crops, and mark new research directions towards a better understanding of the relation between root architecture and yield. We believe that unraveling the role of root architecture in root and tuber crop productivity will improve global food security, especially in regions with marginal soil fertility and low-input agricultural systems.
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Affiliation(s)
- Arthur Q Villordon
- Louisiana State University Agricultural Center Sweet Potato Research Station, Chase, LA 71324, USA.
| | - Idit Ginzberg
- Institute of Plant Sciences, The Volcani Center, Agricultural Research Organization, PO Box 6, Bet Dagan, 50250, Israel
| | - Nurit Firon
- Institute of Plant Sciences, The Volcani Center, Agricultural Research Organization, PO Box 6, Bet Dagan, 50250, Israel
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Kumar S, Shah N, Garg V, Bhatia S. Large scale in-silico identification and characterization of simple sequence repeats (SSRs) from de novo assembled transcriptome of Catharanthus roseus (L.) G. Don. PLANT CELL REPORTS 2014; 33:905-918. [PMID: 24482265 DOI: 10.1007/s00299-014-1569-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 12/17/2013] [Accepted: 01/09/2014] [Indexed: 06/03/2023]
Abstract
Transcriptomic data of C. roseus offering ample sequence resources for providing better insights into gene diversity: large resource of genic SSR markers to accelerate genomic studies and breeding in Catharanthus . Next-generation sequencing is an efficient system for generating high-throughput complete transcripts/genes and developing molecular markers. We present here the transcriptome sequencing of a 26-day-old Catharanthus roseus seedling tissue using Illumina GAIIX platform that resulted in a total of 3.37 Gb of nucleotide sequence data comprising 29,964,104 reads which were de novo assembled into 26,581 unigenes. Based on similarity searches 58 % of the unigenes were annotated of which 13,580 unique transcripts were assigned 5016 gene ontology terms. Further, 7,687 of the unigenes were found to have Cluster of Orthologous Group classifications, and 4,006 were assigned to 289 Kyoto Encyclopedia of Genes and Genome pathways. Also, 5,221 (19.64 %) of transcripts were distributed to 81 known transcription factor (TF) families. In-silico analysis of the transcriptome resulted in identification of 11,004 SSRs in 26.62 % transcripts from which 2,520 SSR markers were designed which exhibited a non-random pattern of distribution. The most abundant was the trinucleotide repeats (AAG/CTT) followed by the dinucleotide repeats (AG/CT). Location specific analysis of SSRs revealed that SSRs were preferentially associated with the 5'-UTRs with a predicted role in regulation of gene expression. A PCR validation of a set of 48 primers revealed 97.9 % successful amplification, and 76.6 % of them showed polymorphism across different Catharanthus species as well as accessions of C. roseus. In summary, this study will provide an insight into understanding the seedling development and resources for novel gene discovery and SSR development for utilization in marker-assisted selective breeding in C. roseus.
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Affiliation(s)
- Santosh Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi, 110067, India
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Li R, Han Y, Lv P, Du R, Liu G. Molecular mapping of the brace root traits in sorghum (Sorghum bicolor L. Moench). BREEDING SCIENCE 2014; 64:193-8. [PMID: 24987306 PMCID: PMC4065327 DOI: 10.1270/jsbbs.64.193] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 02/16/2014] [Indexed: 05/23/2023]
Abstract
The presence and morphology of plant brace roots are important root architecture traits. Brace roots contribute significantly to effective anchorage and water and nutrient uptake during late growth and development, and more importantly, have a substantial influence on grain yield under soil flooding or water limited conditions. However, little is known about the genetic mechanisms that underlie brace root traits. In this study, quantitative trait loci (QTLs) for presence of brace roots from the sorghum landrace "Sansui" were mapped and associated molecular markers were identified. A linkage map was constructed with 109 assigned simple sequence repeat markers using a F2 mapping population derived from the cross Sansui/Jiliang 2. Two QTLs associated with presence of brace roots were localized on chromosomes 6 and 7. The major QTL on chromosome 7 between markers Dsenhsbm7 and Xcup 70 explained about 52.5% of the phenotypic variation, and the minor QTL on chromosome 6 was flanked by Xtxp127 and Xtxp6 and accounted for 7.0% of phenotypic variation. These results will provide information for the improvement of sorghum root architecture associated with brace roots.
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Affiliation(s)
- Ronggai Li
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences,
Shijiazhuang 050031,
China
- School of Biological Sciences, University of Aberdeen,
Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ,
UK
| | - Yucui Han
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences,
Shijiazhuang 050031,
China
| | - Peng Lv
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences,
Shijiazhuang 050031,
China
| | - Ruiheng Du
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences,
Shijiazhuang 050031,
China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences,
Shijiazhuang 050031,
China
- Corresponding author (e-mail: )
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Jin F, Hu L, Yuan D, Xu J, Gao W, He L, Yang X, Zhang X. Comparative transcriptome analysis between somatic embryos (SEs) and zygotic embryos in cotton: evidence for stress response functions in SE development. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:161-73. [PMID: 24112122 DOI: 10.1111/pbi.12123] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/14/2013] [Accepted: 08/15/2013] [Indexed: 05/18/2023]
Abstract
As a product of asexual reproduction in plants, the somatic embryo (SE) differentiates into a new plantlet via a zygotic embryogenesis-like process. Here, we present the phenotypic and cellular differences between SEs and zygotic embryos (ZEs) revealed by histological section scanning using three parallel development stages of the two types of embryos of cotton (Gossypium hirsutum cv. YZ1), including globular, torpedo and cotyledonary-stages. To identify the molecular characteristics of SE development in cotton, the digital gene expression system was used to profile the genes active during SE and ZE development. A total of 4242 differentially expressed genes (DEGs) were identified in at least one developmental stage. Expression pattern and functional classification analysis based on these DEGs reveals that SE development exhibits a transcriptional activation of stress responses. RT-PCR analysis further confirmed enhanced expression levels of stress-related genes in SEs than in ZEs. Experimental stress treatment, induced by NaCl and ABA, accelerated SE development and increased the transcription of genes related to stress response, in parallel with decelerated proliferation of embryogenic calluses under stress treatment. Our data reveal that SE development involves the activation of stress responses, which we suggest may regulate the balance between cell proliferation and differentiation. These results provide new insight into the molecular mechanisms of SE development and suggest strategies that can be used for regulating the developmental processes of somatic embryogenesis.
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Affiliation(s)
- Fangyan Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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25
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Gao J, Chen Z, Luo M, Peng H, Lin H, Qin C, Yuan G, Shen Y, Ding H, Zhao M, Pan G, Zhang Z. Genome expression profile analysis of the maize sheath in response to inoculation to R. solani. Mol Biol Rep 2014; 41:2471-83. [PMID: 24420865 PMCID: PMC3968446 DOI: 10.1007/s11033-014-3103-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 01/06/2014] [Indexed: 12/27/2022]
Abstract
Currently, the molecular regulation mechanisms of disease-resistant involved in maize leaf sheaths infected by banded leaf and sheath blight (BLSB) are poorly known. To gain insight into the transcriptome dynamics that are associated with their disease-resistant, genome-wide gene expression profiling was conducted by Solexa sequencing. More than four million tags were generated from sheath tissues without any leaf or development leaf, including 193,222 and 204,824 clean tags in the two libraries, respectively. Of these, 82,864 (55.4 %) and 91,678 (51.5 %) tags were matched to the reference genes. The most differentially expressed tags with log2 ratio >2 or <-2 (P < 0.001) were further analyzed, representing 1,476 up-regulated and 1,754 down-regulated genes, except for unknown transcripts, which were classified into 11 functional categories. The most enriched categories were those of metabolism, signal transduction and cellular transport. Next, the expression patterns of 12 genes were assessed by quantitative real-time PCR, and it is showed the results were general agreement with the Solexa analysis, although the degree of change was lower in amplitude. In conclusion, we first reveal the complex changes in the transcriptome during the early development of maize sheath infected by BLSB and provide a comprehensive set of data that are essential for understanding its molecular regulation mechanism.
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Affiliation(s)
- Jian Gao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Zhe Chen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Mao Luo
- Drug Discovery Research Center of Luzhou Medical College, Luzhou, 646000 Sichuan China
| | - Hua Peng
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Haijian Lin
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Cheng Qin
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Guangsheng Yuan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Haiping Ding
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Maojun Zhao
- Life Science College of Sichuan Agricultural University, Ya’an, 625014 Sichuan China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Zhiming Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
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Peng Z, Zhang C, Zhang Y, Hu T, Mu S, Li X, Gao J. Transcriptome sequencing and analysis of the fast growing shoots of moso bamboo (Phyllostachys edulis). PLoS One 2013; 8:e78944. [PMID: 24244391 PMCID: PMC3820679 DOI: 10.1371/journal.pone.0078944] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/17/2013] [Indexed: 01/23/2023] Open
Abstract
Background The moso bamboo, a large woody bamboo with the highest ecological, economic, and cultural value of all bamboos, has one of the highest growth speeds in the world. Genetic research into moso bamboo has been scarce, partly because of the lack of previous genomic resources. In the present study, for the first time, we performed de novo transcriptome sequencing and mapped to the moso bamboo genomic resources (reference genome and genes) to produce a comprehensive dataset for the fast growing shoots of moso bamboo. Results The fast growing shoots mixed with six different heights and culms after leaf expansion of moso bamboo transcriptome were sequenced using the Illumina HiSeq™ 2000 sequencing platform, respectively. More than 80 million reads including 65,045,670 and 68,431,884 clean reads were produced in the two libraries. More than 81% of the reads were matched to the reference genome, and nearly 50% of the reads were matched to the reference genes. The genes with log 2 ratio > 2 or < −2 (P<0.001) were characterized as the most differentially expressed genes. 6,076 up-regulated and 4,613 down-regulated genes were classified into functional categories. Candidate genes which mainly involved transcript factors, plant hormones, cell cycle regulation, cell wall metabolism and cell morphogenesis genes were further analyzed and they may form a network that regulates the fast growth of moso bamboo shoots. Conclusion Firstly, our data provides the most comprehensive transcriptomic resource for moso bamboo to date. Candidate genes have been identified and they are potentially involved in the growth and development of moso bamboo. The results give a better insight into the mechanisms of moso bamboo shoots rapid growth and provide gene resources for improving plant growth.
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Affiliation(s)
- Zhenhua Peng
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Chunling Zhang
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Ying Zhang
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Tao Hu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Shaohua Mu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Xueping Li
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Jian Gao
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
- * E-mail:
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27
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Zhong W, Gao Z, Zhuang W, Shi T, Zhang Z, Ni Z. Genome-wide expression profiles of seasonal bud dormancy at four critical stages in Japanese apricot. PLANT MOLECULAR BIOLOGY 2013; 83:247-64. [PMID: 23756818 DOI: 10.1007/s11103-013-0086-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 06/01/2013] [Indexed: 05/08/2023]
Abstract
Dormancy is one of the most important adaptive mechanisms developed by perennial plants. To reveal the comprehensive mechanism of seasonal bud dormancy at four critical stages in Japanese apricot (Prunus persica), we applied Illumina sequencing to study differentially expressed genes (DEGs) at the transcriptional level. As a result, 19,759, 16,375, 19,749 and 20,800 tag-mapped genes were sequenced from libraries of paradormancy (R1), endodormancy (R2), ecodormancy (R3) and dormancy release (R4) stages based on the P. persica genome. Moreover, 6,199, 5,539, and 5,317 genes were differentially expressed in R1 versus R2, R2 versus R3, and R3 versus R4, respectively. Gene Ontology analysis of dormancy-related genes showed that these were mainly related to the cytoplasm, cytoplasmic part metabolism, intracellular metabolism and membrane-bound organelle metabolism. Pathway-enrichment annotation revealed that highly ranked genes were involved in ribosome pathways and protein processing in the endoplasmic reticulum. The results demonstrated that hormone response genes such as auxin, abscisic acid, ethylene and jasmonic acid, as well as zinc finger family protein genes are possibly involved in seasonal bud dormancy in Japanese apricot. The expression patterns of DEGs were verified using real-time quantitative RT-PCR. These results contribute to further understanding of the mechanism of bud dormancy in Japanese apricot.
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Affiliation(s)
- Wenjun Zhong
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, People's Republic of China
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28
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Li J, Wang L, Zhan Q, Liu Y, Fu B, Wang C. Sorghum bmr6 mutant analysis demonstrates that a shared MYB1 transcription factor binding site in the promoter links the expression of genes in related pathways. Funct Integr Genomics 2013; 13:445-53. [PMID: 24045932 DOI: 10.1007/s10142-013-0335-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 08/23/2013] [Accepted: 09/09/2013] [Indexed: 11/29/2022]
Abstract
Sorghum is not only an important cereal crop but also a biofuel crop. The sorghum brown midrib mutant 6 (bmr6) has a reduced lignin content in the cell walls and vascular tissues, which could potentially be advantageous for cellulosic biofuel production. Meanwhile, both dry matter yield and plant height were decreased in the bmr6 mutant. To identify genes affected in the mutant, differential gene expression analysis was performed for bmr6 and the wild type. As a result, a total of 1,052 differentially expressed genes were detected between the two samples, of which 166 genes were downregulated and 886 genes were upregulated. Five hundred seventy-nine of the 1,052 differentially expressed genes could be assigned to 154 documented pathways. These pathways mainly included primary and secondary metabolism. Therefore, mutation of the bmr6 gene, which impaired the biosynthesis of lignin, ultimately affected the expression of these genes associated with the growth and development of sorghum. Except for the bmr6 gene, 11 key enzyme genes of monolignols biosynthesis were upregulated. Promoter analysis identified that these genes have common MYB sites. It revealed that a feedback mechanism existed in the pathway and a MYB1 transcription factor (Sb02g031190) could associate with the upregulation of these genes in sorghum. In this study, we investigated gene expressions at a global level in sorghum bmr6 mutant and provided valuable insights into the mechanisms of lignin biosynthesis.
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Affiliation(s)
- Jieqin Li
- College of Plant Science, Anhui Science and Technology University, Fengyang, People's Republic of China
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29
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Verma P, Shah N, Bhatia S. Development of an expressed gene catalogue and molecular markers from the de novo assembly of short sequence reads of the lentil (Lens culinaris Medik.) transcriptome. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:894-905. [PMID: 23759076 DOI: 10.1111/pbi.12082] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 04/10/2013] [Accepted: 04/15/2013] [Indexed: 05/23/2023]
Abstract
Genomic resources such as ESTs, molecular markers and linkage maps are essential for crop improvement. However, these resources are still limited in important legumes such as lentil (Lens culinaris Medik.), which is valued world wide as a rich source of dietary protein. In this study, the de novo transcriptome assembly of 119,855,798 short reads, generated by Illumina paired-end sequencing, was performed using various assembly programs. This resulted in 42,196 nonredundant high-quality transcripts of average length 810 bases, N50 value of 1,432 and an average expression per transcript of 26.21 rpkm reads per kilobase per million(RPKM). Similarity search with the unigenes and protein sequences of other plants resulted in maximum similarity with soybean. A total of 20,009 nonredundant transcripts showed similarity with the UniProtKB database and of these, 18,064 transcripts were grouped into three main GO categories, that is, biological process (15,126), molecular function (15,505) and cellular component (9,434). Annotated transcripts were mapped to 289 predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 8,893 transcripts were classified into 24 functional categories based on Cluster of Orthologous Groups (COG) of proteins. Mining the data set for the presence of SSRs resulted in 8,722 SSRs with a frequency occurrence of one SSR per 3.92 kb. From these, 5,673 SSR primer pairs were designed, and a subset of these were utilized for diversity analysis. This study, which provides a large data set of annotated transcripts and gene-based SSR markers, would serve as a foundation for various applications in lentil breeding and genetics.
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Affiliation(s)
- Priyanka Verma
- National Institute of Plant Genome Research, New Delhi, India
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30
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Orman-Ligeza B, Parizot B, Gantet PP, Beeckman T, Bennett MJ, Draye X. Post-embryonic root organogenesis in cereals: branching out from model plants. TRENDS IN PLANT SCIENCE 2013; 18:459-67. [PMID: 23727199 DOI: 10.1016/j.tplants.2013.04.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/23/2013] [Accepted: 04/29/2013] [Indexed: 05/07/2023]
Abstract
The root architecture of higher plants is amazingly diverse. In this review, we compare the lateral root developmental programme in cereals and Arabidopsis thaliana. In cereals, cells in the endodermis are recruited to form the new root cap and overlying cortical cells divide to facilitate the emergence of the lateral root primordium. The TIR1/ABF2 auxin receptors and the AUX/IAA, ARF, and LBD transcriptional regulatory proteins are conserved in cereals and Arabidopsis. Several elements of this regulatory network are common to lateral and crown roots in cereals. Also, the ground meristem from which crown roots differentiate shows similarities with the root pericycle. Studies in cereals promise to give complementary insights into the mechanisms regulating the development of post-embryonic roots in plants.
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Affiliation(s)
- Beata Orman-Ligeza
- Université catholique de Louvain, Earth and Life Institute, Louvain-la-Neuve, Belgium
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31
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Ma J, Wei H, Liu J, Song M, Pang C, Wang L, Zhang W, Fan S, Yu S. Selection and characterization of a novel photoperiod-sensitive male sterile line in upland cotton. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:608-18. [PMID: 23691935 DOI: 10.1111/jipb.12067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 05/15/2013] [Indexed: 05/08/2023]
Abstract
Upland cotton (Gossypium hirsutum L.) shows strong heterosis. However, heterosis is not widely utilized owing to the high cost of hybrid seed production. Creation of a photoperiod-sensitive genetic male sterile line could substantially reduce the cost of hybrid seed production in upland cotton. Such a mutant with virescent marker was found by space mutation in near-earth orbit and its traits had been stable after 4 years of selection in Anyang and Sanya, China. This mutant was fertile with an 11-12.5 h photoperiod when the temperature was higher than 21.5 °C and was sterile with a 13-14.5 h photoperiod. Genetic analysis indicated that both traits were controlled by a single recessive gene or two closely linked genes. Also, the cytological observations and transcriptome profiling analysis showed that the degradation of pollen grain cytoplasm should be the primary reason why the mutant line were male sterile under long-day conditions.
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Affiliation(s)
- Jianhui Ma
- State Key Laboratory of Cotton Biology, the Institute of Cotton Research, the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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Shen Y, Zhang Y, Chen J, Lin H, Zhao M, Peng H, Liu L, Yuan G, Zhang S, Zhang Z, Pan G. Genome expression profile analysis reveals important transcripts in maize roots responding to the stress of heavy metal Pb. PHYSIOLOGIA PLANTARUM 2013; 147:270-82. [PMID: 22747913 DOI: 10.1111/j.1399-3054.2012.01670.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 06/06/2012] [Indexed: 05/10/2023]
Abstract
Lead (Pb) has become one of the most abundant heavy metal pollutants of the environment. With its large biomass, maize could be an important object for studying the phytoremediation of Pb-contaminated soil. In our previous research, we screened 19 inbred lines of maize for Pb concentration, and line 178 was identified to be a hyperaccumulator for Pb in both the roots and aboveground parts. To identify important genes and metabolic pathways related to Pb accumulation and tolerance, line 178 was underwent genome expression profile under Pb stress and a control (CK). A total of approximately 11 million cDNA tags were sequenced and 4 665 539 and 4 936 038 clean tags were obtained from the libraries of the test and CK, respectively. In comparison to CK, 2379 and 1832 genes were identified up- or downregulated, respectively, more than fivefolds under Pb stress. Interestingly, all the genes were related to cellular processes and signaling, information storage and processing or metabolism functions. Particularly, the genes involved in posttranslational modification, protein turnover and chaperones; signal transduction, carbohydrate transport and metabolism; and lipid transport and metabolism significantly changed under the treatment. In addition, seven pathways including ribosome, photosynthesis, and carbon fixation were affected significantly, with 118, 12, 34, 21, 18, 72 and 43 differentially expressed genes involved. The significant upregulation of the ribosome pathway may reveal an important secret for Pb tolerance of line 178. And the sharp increase of laccase transcripts and metal ion transporters were suggested to account in part for Pb hyperaccumulation in the line.
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Affiliation(s)
- Yaou Shen
- Maize Research Institute of Sichuan Agricultural University, Ya'an, 625014, China
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Liu P, Yan K, Lei YX, Xu R, Zhang YM, Yang GD, Huang JG, Wu CA, Zheng CC. Transcript profiling of microRNAs during the early development of the maize brace root via Solexa sequencing. Genomics 2013; 101:149-56. [DOI: 10.1016/j.ygeno.2012.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 09/29/2012] [Accepted: 11/02/2012] [Indexed: 01/13/2023]
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Ma J, Wei H, Song M, Pang C, Liu J, Wang L, Zhang J, Fan S, Yu S. Transcriptome profiling analysis reveals that flavonoid and ascorbate-glutathione cycle are important during anther development in Upland cotton. PLoS One 2012; 7:e49244. [PMID: 23155472 PMCID: PMC3498337 DOI: 10.1371/journal.pone.0049244] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 10/04/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Previous transcriptome profiling studies have investigated the molecular mechanisms of pollen and anther development, and identified many genes involved in these processes. However, only 51 anther ESTs of Upland cotton (Gossypium hirsutum) were found in NCBI and there have been no reports of transcriptome profiling analyzing anther development in Upland cotton, a major fiber crop in the word. METHODOLOGY/PRINCIPAL FINDING Ninety-eight hundred and ninety-six high quality ESTs were sequenced from their 3'-ends and assembled into 6,643 unigenes from a normalized, full-length anther cDNA library of Upland cotton. Combined with previous sequenced anther-related ESTs, 12,244 unigenes were generated as the reference genes for digital gene expression (DGE) analysis. The DGE was conducted on anthers that were isolated at tetrad pollen (TTP), uninucleate pollen (UNP), binucleate pollen (BNP) and mature pollen (MTP) periods along with four other tissues, i.e., roots (RO), stems (ST), leaves (LV) and embryos (EB). Through transcriptome profiling analysis, we identified 1,165 genes that were enriched at certain anther development periods, and many of them were involved in starch and sucrose metabolism, pentose and glucuronate interconversion, flavonoid biosynthesis, and ascorbate and aldarate metabolism. CONCLUSIONS/SIGNIFICANCE We first generated a normalized, full-length cDNA library from anthers and performed transcriptome profiling analysis of anther development in Upland cotton. From these results, 10,178 anther expressed genes were identified, among which 1,165 genes were stage-enriched in anthers. And many of these stage-enriched genes were involved in some important processes regulating anther development.
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Affiliation(s)
- Jianhui Ma
- College of Agronomy, Northwest A&F University, Yangling, Shanxi, People's Republic of China
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Meizhen Song
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Ji Liu
- College of Agronomy, Northwest A&F University, Yangling, Shanxi, People's Republic of China
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Long Wang
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
- * E-mail: (SF); (SY)
| | - Shuxun Yu
- College of Agronomy, Northwest A&F University, Yangling, Shanxi, People's Republic of China
- State Key Laboratory of Cotton Biology, The Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
- * E-mail: (SF); (SY)
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35
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Shi T, Gao Z, Wang L, Zhang Z, Zhuang W, Sun H, Zhong W. Identification of differentially-expressed genes associated with pistil abortion in Japanese apricot by genome-wide transcriptional analysis. PLoS One 2012; 7:e47810. [PMID: 23091648 PMCID: PMC3472986 DOI: 10.1371/journal.pone.0047810] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 09/17/2012] [Indexed: 12/05/2022] Open
Abstract
The phenomenon of pistil abortion widely occurs in Japanese apricot, and imperfect flowers with pistil abortion seriously decrease the yield in production. Although transcriptome analyses have been extensively studied in the past, a systematic study of differential gene expression has not been performed in Japanese apricot. To investigate genes related to the pistil development of Japanese apricot, high-throughput sequencing technology (Illumina) was employed to survey gene expression profiles from perfect and imperfect Japanese apricot flower buds. 3,476,249 and 3,580,677 tags were sequenced from two libraries constructed from perfect and imperfect flower buds of Japanese apricot, respectively. There were 689 significant differentially-expressed genes between the two libraries. GO annotation revealed that highly ranked genes were those implicated in small molecule metabolism, cellular component organisation or biogenesis at the cellular level and fatty acid metabolism. According to the results, we assumed that late embryogenesis abundant protein (LEA), Dicer-like 3 (DCL3) Xyloglucan endotransglucosylase/hydrolase 2 (XTH2), Pectin lyase-like superfamily protein (PPME1), Lipid transfer protein 3 (LTP3), Fatty acid biosynthesis 1 (FAB1) and Fatty acid desaturase 5 (FAD5) might have relationships with the pistil abortion in Japanese apricot. The expression patterns of 36 differentially expressed genes were confirmed by real-time (RT)-PCR. This is the first report of the Illumina RNA-seq technique being used for the analysis of differentially-expressed gene profiles related to pistil abortion that both computationally and experimentally provides valuable information for the further functional characterisation of genes associated with pistil development in woody plants.
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Affiliation(s)
- Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
- * E-mail:
| | - Liangju Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Zhen Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Weibing Zhuang
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Hailong Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Wenjun Zhong
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
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36
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Forestan C, Varotto S. The role of PIN auxin efflux carriers in polar auxin transport and accumulation and their effect on shaping maize development. MOLECULAR PLANT 2012; 5:787-98. [PMID: 22186966 DOI: 10.1093/mp/ssr103] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In plants, proper seed development and the continuing post-embryonic organogenesis both require that different cell types are correctly differentiated in response to internal and external stimuli. Among internal stimuli, plant hormones and particularly auxin and its polar transport (PAT) have been shown to regulate a multitude of plant physiological processes during vegetative and reproductive development. Although our current auxin knowledge is almost based on the results from researches on the eudicot Arabidopsis thaliana, during the last few years, many studies tried to transfer this knowledge from model to crop species, maize in particular. Applications of auxin transport inhibitors, mutant characterization, and molecular and cell biology approaches, facilitated by the sequencing of the maize genome, allowed the identification of genes involved in auxin metabolism, signaling, and particularly in polar auxin transport. PIN auxin efflux carriers have been shown to play an essential role in regulating PAT during both seed and post-embryonic development in maize. In this review, we provide a summary of the recent findings on PIN-mediated polar auxin transport during maize development. Similarities and differences between maize and Arabidopsis are analyzed and discussed, also considering that their different plant architecture depends on the differentiation of structures whose development is controlled by auxins.
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Affiliation(s)
- Cristian Forestan
- Department of Environmental Agronomy and Crop Science-University of Padova, Legnaro (PD), Italy.
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37
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Shen Y, Jiang Z, Yao X, Zhang Z, Lin H, Zhao M, Liu H, Peng H, Li S, Pan G. Genome expression profile analysis of the immature maize embryo during dedifferentiation. PLoS One 2012; 7:e32237. [PMID: 22448216 PMCID: PMC3308947 DOI: 10.1371/journal.pone.0032237] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Accepted: 01/25/2012] [Indexed: 11/17/2022] Open
Abstract
Maize is one of the most important cereal crops worldwide and one of the primary targets of genetic manipulation, which provides an excellent way to promote its production. However, the obvious difference of the dedifferentiation frequency of immature maize embryo among various genotypes indicates that its genetic transformation is dependence on genotype and immature embryo-derived undifferentiated cells. To identify important genes and metabolic pathways involved in forming of embryo-derived embryonic calli, in this study, DGE (differential gene expression) analysis was performed on stages I, II, and III of maize inbred line 18-599R and corresponding control during the process of immature embryo dedifferentiation. A total of ∼21 million cDNA tags were sequenced, and 4,849,453, 5,076,030, 4,931,339, and 5,130,573 clean tags were obtained in the libraries of the samples and the control, respectively. In comparison with the control, 251, 324 and 313 differentially expressed genes (DEGs) were identified in the three stages with more than five folds, respectively. Interestingly, it is revealed that all the DEGs are related to metabolism, cellular process, and signaling and information storage and processing functions. Particularly, the genes involved in amino acid and carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis and signal transduction mechanism have been significantly changed during the dedifferentiation. To our best knowledge, this study is the first genome-wide effort to investigate the transcriptional changes in dedifferentiation immature maize embryos and the identified DEGs can serve as a basis for further functional characterization.
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Affiliation(s)
- Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute of Sichuan Agricultural University, Ministry of Agriculture, Wenjiang, People's Republic of China
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38
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Kyndt T, Denil S, Haegeman A, Trooskens G, De Meyer T, Van Criekinge W, Gheysen G. Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2141-57. [PMID: 22213813 DOI: 10.1093/jxb/err435] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Despite the major physiological dissimilarities between mature root regions and their tips, differences in their gene expression profiles remain largely unexplored. In this research, the transcriptome of rice (Oryza sativa L. subsp. japonica) mature root tissue and root tips was monitored using mRNA-Seq at two time points. Almost 50 million 76 bp reads were mapped onto the rice genome sequence, expression patterns for different tissues and time points were investigated, and at least 1106 novel transcriptionally active regions (nTARs) expressed in rice root tissue were detected. More than 30 000 genes were found to be expressed in rice roots, among which were 1761 root-enriched and 306 tip-enriched transcripts. Mature root tissue appears to respond more strongly to external stimuli than tips, showing a higher expression of, for instance, auxin-responsive and abscisic acid-responsive genes, as well as the phenylpropanoid pathway and photosynthesis upon light. The root tip-enriched transcripts are mainly involved in mitochondrial electron transport, organelle development, secondary metabolism, DNA replication and metabolism, translation, and cellular component organization. During root maturation, genes involved in cell wall biosynthesis and modification, response to oxidative stress, and secondary metabolism were activated. For some nTARs, a potential role in root development can be put forward based on homology to genes involved in CLAVATA signalling, cell cycle regulators, and hormone signalling. A subset of differentially expressed genes and novel transcripts was confirmed using (quantitative) reverse transcription-PCR. These results uncover previously unrecognized tissue-specific expression profiles and provide an interesting starting point to study the different regulation of transcribed regions of these tissues.
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Affiliation(s)
- Tina Kyndt
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, Ghent, Belgium
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39
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Li H, Dong Y, Yang J, Liu X, Wang Y, Yao N, Guan L, Wang N, Wu J, Li X. De novo transcriptome of safflower and the identification of putative genes for oleosin and the biosynthesis of flavonoids. PLoS One 2012; 7:e30987. [PMID: 22363528 PMCID: PMC3283594 DOI: 10.1371/journal.pone.0030987] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 12/29/2011] [Indexed: 11/18/2022] Open
Abstract
Safflower (Carthamus tinctorius L.) is one of the most extensively used oil crops in the world. However, little is known about how its compounds are synthesized at the genetic level. In this study, Solexa-based deep sequencing on seed, leaf and petal of safflower produced a de novo transcriptome consisting of 153,769 unigenes. We annotated 82,916 of the unigenes with gene annotation and assigned functional terms and specific pathways to a subset of them. Metabolic pathway analysis revealed that 23 unigenes were predicted to be responsible for the biosynthesis of flavonoids and 8 were characterized as seed-specific oleosins. In addition, a large number of differentially expressed unigenes, for example, those annotated as participating in anthocyanin and chalcone synthesis, were predicted to be involved in flavonoid biosynthesis pathways. In conclusion, the de novo transcriptome investigation of the unique transcripts provided candidate gene resources for studying oleosin-coding genes and for investigating genes related to flavonoid biosynthesis and metabolism in safflower.
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Affiliation(s)
- Haiyan Li
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China
- College of Life Sciences, Jilin Agricultural University, Changchun, Jilin, China
| | - Yuanyuan Dong
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China
| | - Jing Yang
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China
| | - Xiuming Liu
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China
- College of Life Sciences, Jilin Agricultural University, Changchun, Jilin, China
| | - Yanfang Wang
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China
| | - Na Yao
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China
| | - Lili Guan
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China
| | - Nan Wang
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China
| | - Jinyu Wu
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China
- Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou, China
- * E-mail: (JW); (X. Li)
| | - Xiaokun Li
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China
- * E-mail: (JW); (X. Li)
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Henry RJ. Next-generation sequencing for understanding and accelerating crop domestication. Brief Funct Genomics 2011; 11:51-6. [PMID: 22025450 DOI: 10.1093/bfgp/elr032] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Next generation Sequencing (NGS) provides a powerful tool for discovery of domestication genes in crop plants and their wild relatives. The accelerated domestication of new plant species as crops may be facilitated by this knowledge. Re-sequencing of domesticated genotypes can identify regions of low diversity associated with domestication. Species-specific data can be obtained from related wild species by whole-genome shot-gun sequencing. This sequence data can be used to design species specific polymerase chain reaction (PCR) primers. Sequencing of the products of PCR amplification of target genes can be used to explore genetic variation in large numbers of genes and gene families. Novel allelic variation in close or distant relatives can be characterized by NGS. Examples of recent applications of NGS to capture of genetic diversity for crop improvement include rice, sugarcane and Eucalypts. Populations of large numbers of individuals can be screened rapidly. NGS supports the rapid domestication of new plant species and the efficient identification and capture of novel genetic variation from related species.
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Affiliation(s)
- Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia.
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41
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Li X, Wang X, Zhang S, Liu D, Duan Y, Dong W. Comparative profiling of the transcriptional response to soybean cyst nematode infection of soybean roots by deep sequencing. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4510-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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