1
|
Ahmad M, Waraich EA, Skalicky M, Hussain S, Zulfiqar U, Anjum MZ, Habib ur Rahman M, Brestic M, Ratnasekera D, Lamilla-Tamayo L, Al-Ashkar I, EL Sabagh A. Adaptation Strategies to Improve the Resistance of Oilseed Crops to Heat Stress Under a Changing Climate: An Overview. FRONTIERS IN PLANT SCIENCE 2021; 12:767150. [PMID: 34975951 PMCID: PMC8714756 DOI: 10.3389/fpls.2021.767150] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/11/2021] [Indexed: 05/16/2023]
Abstract
Temperature is one of the decisive environmental factors that is projected to increase by 1. 5°C over the next two decades due to climate change that may affect various agronomic characteristics, such as biomass production, phenology and physiology, and yield-contributing traits in oilseed crops. Oilseed crops such as soybean, sunflower, canola, peanut, cottonseed, coconut, palm oil, sesame, safflower, olive etc., are widely grown. Specific importance is the vulnerability of oil synthesis in these crops against the rise in climatic temperature, threatening the stability of yield and quality. The natural defense system in these crops cannot withstand the harmful impacts of heat stress, thus causing a considerable loss in seed and oil yield. Therefore, a proper understanding of underlying mechanisms of genotype-environment interactions that could affect oil synthesis pathways is a prime requirement in developing stable cultivars. Heat stress tolerance is a complex quantitative trait controlled by many genes and is challenging to study and characterize. However, heat tolerance studies to date have pointed to several sophisticated mechanisms to deal with the stress of high temperatures, including hormonal signaling pathways for sensing heat stimuli and acquiring tolerance to heat stress, maintaining membrane integrity, production of heat shock proteins (HSPs), removal of reactive oxygen species (ROS), assembly of antioxidants, accumulation of compatible solutes, modified gene expression to enable changes, intelligent agricultural technologies, and several other agronomic techniques for thriving and surviving. Manipulation of multiple genes responsible for thermo-tolerance and exploring their high expressions greatly impacts their potential application using CRISPR/Cas genome editing and OMICS technology. This review highlights the latest outcomes on the response and tolerance to heat stress at the cellular, organelle, and whole plant levels describing numerous approaches applied to enhance thermos-tolerance in oilseed crops. We are attempting to critically analyze the scattered existing approaches to temperature tolerance used in oilseeds as a whole, work toward extending studies into the field, and provide researchers and related parties with useful information to streamline their breeding programs so that they can seek new avenues and develop guidelines that will greatly enhance ongoing efforts to establish heat stress tolerance in oilseeds.
Collapse
Affiliation(s)
- Muhammad Ahmad
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
- Horticultural Sciences Department, Tropical Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Homestead, FL, United States
| | | | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Saddam Hussain
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Usman Zulfiqar
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Zohaib Anjum
- Department of Forestry and Range Management, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Habib ur Rahman
- Department of Agronomy, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University Bonn, Bonn, Germany
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Slovakia
| | - Disna Ratnasekera
- Department of Agricultural Biology, Faculty of Agriculture, University of Ruhuna, Kamburupitiya, Sri Lanka
| | - Laura Lamilla-Tamayo
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Ibrahim Al-Ashkar
- Department of Plant Production, College of Food and Agriculture, King Saud University, Riyadh, Saudi Arabia
- Agronomy Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Ayman EL Sabagh
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, Turkey
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Shaikh, Egypt
| |
Collapse
|
2
|
Bengoa Luoni SA, Cenci A, Moschen S, Nicosia S, Radonic LM, Sabio J, Garcia, Langlade NB, Vile D, Rovere CV, Fernandez P. Genome-wide and comparative phylogenetic analysis of senescence-associated NAC transcription factors in sunflower (Helianthus annuus). BMC Genomics 2021; 22:893. [PMID: 34906091 PMCID: PMC8670195 DOI: 10.1186/s12864-021-08199-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/19/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Leaf senescence delay impacts positively in grain yield by maintaining the photosynthetic area during the reproductive stage and during grain filling. Therefore a comprehensive understanding of the gene families associated with leaf senescence is essential. NAC transcription factors (TF) form a large plant-specific gene family involved in regulating development, senescence, and responses to biotic and abiotic stresses. The main goal of this work was to identify sunflower NAC TF (HaNAC) and their association with senescence, studying their orthologous to understand possible functional relationships between genes of different species. RESULTS To clarify the orthologous relationships, we used an in-depth comparative study of four divergent taxa, in dicots and monocots, with completely sequenced genomes (Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa). These orthologous groups provide a curated resource for large scale protein sequence annotation of NAC TF. From the 151 HaNAC genes detected in the latest version of the sunflower genome, 50 genes were associated with senescence traits. These genes showed significant differential expression in two contrasting lines according to an RNAseq assay. An assessment of overexpressing the Arabidopsis line for HaNAC001 (a gene of the same orthologous group of Arabidopsis thaliana ORE1) revealed that this line displayed a significantly higher number of senescent leaves and a pronounced change in development rate. CONCLUSIONS This finding suggests HaNAC001 as an interesting candidate to explore the molecular regulation of senescence in sunflower.
Collapse
Affiliation(s)
- Sofia A Bengoa Luoni
- Instituto de Agrobiotecnología y Biología Molecular, INTA-Castelar, Buenos Aires, Argentina
| | | | - Sebastian Moschen
- Estación Experimental Agropecuaria Famaillá, INTA-Famaillá, Tucumán, Argentina
| | - Salvador Nicosia
- Instituto de Agrobiotecnología y Biología Molecular, INTA-Castelar, Buenos Aires, Argentina
| | - Laura M Radonic
- Instituto de Agrobiotecnología y Biología Molecular, INTA-Castelar, Buenos Aires, Argentina
| | | | - Garcia
- Instituto de Agrobiotecnología y Biología Molecular, INTA-Castelar, Buenos Aires, Argentina
| | | | - Denis Vile
- LEPSE, Université de Montpellier, INRAE, Montpellier, France
| | - Cecilia Vazquez Rovere
- Instituto de Agrobiotecnología y Biología Molecular, INTA-Castelar, Buenos Aires, Argentina
| | - Paula Fernandez
- Instituto de Agrobiotecnología y Biología Molecular, INTA-Castelar, Buenos Aires, Argentina.
| |
Collapse
|
3
|
Gene Expression Correlation Analysis Reveals MYC-NAC Regulatory Network in Cotton Pigment Gland Development. Int J Mol Sci 2021; 22:ijms22095007. [PMID: 34066899 PMCID: PMC8125883 DOI: 10.3390/ijms22095007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 11/17/2022] Open
Abstract
Plant NAC (NAM, ATAF1/2, and CUC2) family is involved in various development processes including Programmed Cell Death (PCD) associated development. However, the relationship between NAC family and PCD-associated cotton pigment gland development is largely unknown. In this study, we identified 150, 153 and 299 NAC genes in newly updated genome sequences of G. arboreum, G. raimondii and G. hirsutum, respectively. All NAC genes were divided into 8 groups by the phylogenetic analysis and most of them were conserved during cotton evolution. Using the vital regulator of gland formation GhMYC2-like as bait, expression correlation analysis screened out 6 NAC genes which were low-expressed in glandless cotton and high-expressed in glanded cotton. These 6 NAC genes acted downstream of GhMYC2-like and were induced by MeJA. Silencing CGF1(Cotton Gland Formation1), another MYC-coding gene, caused almost glandless phenotype and down-regulated expression of GhMYC2-like and the 6 NAC genes, indicating a MYC-NAC regulatory network in gland development. In addition, predicted regulatory mechanism showed that the 6 NAC genes were possibly regulated by light, various phytohormones and transcription factors as well as miRNAs. The interaction network and DNA binding sites of the 6 NAC transcription factors were also predicted. These results laid the foundation for further study of gland-related genes and gland development regulatory network.
Collapse
|
4
|
Bengoa Luoni S, Astigueta FH, Nicosia S, Moschen S, Fernandez P, Heinz R. Transcription Factors Associated with Leaf Senescence in Crops. PLANTS (BASEL, SWITZERLAND) 2019; 8:E411. [PMID: 31614987 PMCID: PMC6843677 DOI: 10.3390/plants8100411] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022]
Abstract
Leaf senescence is a complex mechanism controlled by multiple genetic and environmental variables. Different crops present a delay in leaf senescence with an important impact on grain yield trough the maintenance of the photosynthetic leaf area during the reproductive stage. Additionally, because of the temporal gap between the onset and phenotypic detection of the senescence process, candidate genes are key tools to enable the early detection of this process. In this sense and given the importance of some transcription factors as hub genes in senescence pathways, we present a comprehensive review on senescence-associated transcription factors, in model plant species and in agronomic relevant crops. This review will contribute to the knowledge of leaf senescence process in crops, thus providing a valuable tool to assist molecular crop breeding.
Collapse
Affiliation(s)
- Sofia Bengoa Luoni
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires 1425, Argentina.
| | - Francisco H Astigueta
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires 1425, Argentina.
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires 1650, Argentina.
| | - Salvador Nicosia
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires 1425, Argentina.
- Universidad Nacional de Lujan, Cruce Rutas Nac. 5 y 7, Lujan, Buenos Aires 6700, Argentina.
| | - Sebastian Moschen
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires 1425, Argentina.
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Famaillá, Tucumán 4142, Argentina.
| | - Paula Fernandez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires 1425, Argentina.
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires 1650, Argentina.
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires 1686, Argentina.
| | - Ruth Heinz
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires 1425, Argentina.
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires 1686, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires 1428, Argentina.
| |
Collapse
|
5
|
Raineri J, Campi M, Chan RL, Otegui ME. Maize expressing the sunflower transcription factor HaHB11 has improved productivity in controlled and field conditions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110185. [PMID: 31481205 DOI: 10.1016/j.plantsci.2019.110185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/05/2019] [Accepted: 07/06/2019] [Indexed: 06/10/2023]
Abstract
HaHB11 is a sunflower transcription factor from the homeodomain-leucine zipper I family. Transgenic Arabidopsis plants expressing HaHB11 had larger rosettes and improved seed yield. In this work maize plants from hybrid HiII were transformed with 35S:HaHB11, ZmUBI:HaHB11 and ProHaHB11:HaHB11 and then backcrossed to B73 to obtain a more homozygous inbred phenotype. Transgene expression levels were stable at least during three generations. Greenhouse-grown HaHB11 transgenic lines had larger leaf area and delayed senescence than controls, together with increased total biomass (up to 25%) and seed yield (up to 28%). Field trials conducted with T2 and T4 generations indicated that enhanced leaf area (up to 18%), stem diameter (up to 28%) and total biomass (up to 40%) as well as delayed leaf senescence were maintained among transgenic individuals when upscaling from pots in the greenhouse to communal plants in the field. The T4 field-grown transgenic generation had increased light interception and radiation use efficiency as well as seed yield (43-47% for events driven by the 35S promoter). Results suggest that HaHB11 is a promising tool for crop improvement because differential traits observed in the Arabidopsis model plant were preserved in a crop like maize independently of growth conditions and backcross level.
Collapse
Affiliation(s)
- Jesica Raineri
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral- CONICET, Facultad de Bioquímica y Ciencias Biológicas, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina.
| | - Mabel Campi
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral- CONICET, Facultad de Bioquímica y Ciencias Biológicas, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina.
| | - Raquel L Chan
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral- CONICET, Facultad de Bioquímica y Ciencias Biológicas, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina.
| | - María E Otegui
- CONICET- INTA-FAUBA, Estación Experimental Pergamino, Facultad de Agronomía Universidad de Buenos Aires, Buenos Aires, Argentina.
| |
Collapse
|
6
|
Gezeljeh Ali S, Darvishzadeh R, Ebrahimi A, Bihamta MR. Identification of SSR and retrotransposon-based molecular markers linked to morphological characters in oily sunflower ( $$\textit{Helianthus annuus}$$ Helianthus annuus L.) under natural and water-limited states. J Genet 2018. [DOI: 10.1007/s12041-018-0901-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
7
|
Ali SG, Darvishzadeh R, Ebrahimi A, Bihamta MR. Identification of SSR and retrotransposon-based molecular markers linked to morphological characters in oily sunfl ower (Helianthus annuus L.) under natural and water-limited states. J Genet 2018; 97:189-203. [PMID: 29666338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sunflower is an important source of edible oil. Drought is known as an important factor limiting the growth and productivity of field crops in most parts of the world. Agricultural biotechnology mainly aims at developing crops with higher tolerance to the challenging environmental conditions, such as drought. This study examined a number of morphological characters, along with relative water content (RWC) in 100 inbred sunflower lines. A 10 × 10 simple lattice design with two replications was employed to measure the mentioned parameters under natural and water-limited states during two successive years. In molecular trial, 30 simple sequence repeat (SSR) primer pairs, as well as 14 inter-retrotransposon amplified polymorphism (IRAP) and 14 retrotransposon-microsatellite amplified polymorphism (REMAP) primer combinations were used for DNA fingerprinting of the lines. Most of the examined characters had lower average values under water-limited than natural states. Maximum and minimum reductions were observed in the cases of yield and oil percentage, respectively. The broad-sense heritabilities for all the examined characters were 0.20-0.73 and 0.10-0.34 under natural and water-limited states, respectively. In the studied samples, 8.97% of the 435 possible locus pairs of the SSRs represented significant linkage disequilibrium (LD) levels. In the association analysis using SSR markers, 22 and 21 markers were identified (P ≤ 0.05) for the studied characters under natural and water-limited states, respectively. The corresponding values were 50 and 37 using retrotransposon-based molecular markers. Some detected markers were communal between the characters under water-limited and natural states. This was in line with the phenotypic correlations detected between the characters. Communal markers facilitate the simultaneous selection of several characters and can thus improve the efficacy of selection based on markers in the plant-breeding activities.
Collapse
Affiliation(s)
- Soleimani Gezeljeh Ali
- Faculty of Agriculture and Natural Resources, Science and Research Branch, Islamic Azad University, 14515-775 Tehran, Iran.
| | | | | | | |
Collapse
|
8
|
Zubrzycki JE, Maringolo CA, Filippi CV, Quiróz FJ, Nishinakamasu V, Puebla AF, Di Rienzo JA, Escande A, Lia VV, Heinz RA, Hopp HE, Cervigni GDL, Paniego NB. Main and epistatic QTL analyses for Sclerotinia Head Rot resistance in sunflower. PLoS One 2017; 12:e0189859. [PMID: 29261806 PMCID: PMC5738076 DOI: 10.1371/journal.pone.0189859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 12/04/2017] [Indexed: 02/04/2023] Open
Abstract
Sclerotinia Head Rot (SHR), a disease caused by Sclerotinia sclerotiorum, is one of the most limiting factors in sunflower production. In this study, we identified genomic loci associated with resistance to SHR to support the development of assisted breeding strategies. We genotyped 114 Recombinant Inbred Lines (RILs) along with their parental lines (PAC2 -partially resistant-and RHA266 -susceptible-) by using a 384 single nucleotide polymorphism (SNP) Illumina Oligo Pool Assay to saturate a sunflower genetic map. Subsequently, we tested these lines for SHR resistance using assisted inoculations with S. sclerotiorum ascospores. We also conducted a randomized complete-block assays with three replicates to visually score disease incidence (DI), disease severity (DS), disease intensity (DInt) and incubation period (IP) through four field trials (2010-2014). We finally assessed main effect quantitative trait loci (M-QTLs) and epistatic QTLs (E-QTLs) by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively. As a result of this study, the improved map incorporates 61 new SNPs over candidate genes. We detected a broad range of narrow sense heritability (h2) values (1.86-59.9%) as well as 36 M-QTLs and 13 E-QTLs along 14 linkage groups (LGs). On LG1, LG10, and LG15, we repeatedly detected QTLs across field trials; which emphasizes their putative effectiveness against SHR. In all selected variables, most of the identified QTLs showed high determination coefficients, associated with moderate to high heritability values. Using markers shared with previous Sclerotinia resistance studies, we compared the QTL locations in LG1, LG2, LG8, LG10, LG11, LG15 and LG16. This study constitutes the largest report of QTLs for SHR resistance in sunflower. Further studies focusing on the regions in LG1, LG10, and LG15 harboring the detected QTLs are necessary to identify causal alleles and contribute to unraveling the complex genetic basis governing the resistance.
Collapse
Affiliation(s)
- Jeremías Enrique Zubrzycki
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Carla Andrea Maringolo
- Laboratorio de Patología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Carla Valeria Filippi
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Facundo José Quiróz
- Laboratorio de Patología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Verónica Nishinakamasu
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Andrea Fabiana Puebla
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Julio A. Di Rienzo
- Cátedra de Estadística y Biometría, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Alberto Escande
- Laboratorio de Patología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Verónica Viviana Lia
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ruth Amalia Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Horacio Esteban Hopp
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gerardo D. L. Cervigni
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Centro de Estudios Fotosintéticos y Bioquímicos, Rosario, Santa Fe, Argentina
| | - Norma Beatriz Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
9
|
Moschen S, Di Rienzo JA, Higgins J, Tohge T, Watanabe M, González S, Rivarola M, García-García F, Dopazo J, Hopp HE, Hoefgen R, Fernie AR, Paniego N, Fernández P, Heinz RA. Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.). PLANT MOLECULAR BIOLOGY 2017; 94:549-564. [PMID: 28639116 DOI: 10.1007/s11103-017-0625-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 06/12/2017] [Indexed: 05/19/2023]
Abstract
By integration of transcriptional and metabolic profiles we identified pathways and hubs transcription factors regulated during drought conditions in sunflower, useful for applications in molecular and/or biotechnological breeding. Drought is one of the most important environmental stresses that effects crop productivity in many agricultural regions. Sunflower is tolerant to drought conditions but the mechanisms involved in this tolerance remain unclear at the molecular level. The aim of this study was to characterize and integrate transcriptional and metabolic pathways related to drought stress in sunflower plants, by using a system biology approach. Our results showed a delay in plant senescence with an increase in the expression level of photosynthesis related genes as well as higher levels of sugars, osmoprotectant amino acids and ionic nutrients under drought conditions. In addition, we identified transcription factors that were upregulated during drought conditions and that may act as hubs in the transcriptional network. Many of these transcription factors belong to families implicated in the drought response in model species. The integration of transcriptomic and metabolomic data in this study, together with physiological measurements, has improved our understanding of the biological responses during droughts and contributes to elucidate the molecular mechanisms involved under this environmental condition. These findings will provide useful biotechnological tools to improve stress tolerance while maintaining crop yield under restricted water availability.
Collapse
Affiliation(s)
- Sebastián Moschen
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Julio A Di Rienzo
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Janet Higgins
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Sergio González
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Máximo Rivarola
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Francisco García-García
- Computational Genomics Department, Centro de Investigación Príncipe Felipe. Functional Genomics Node (INB-ELIXIR-es). Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, 46012, Spain
| | - Joaquin Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe. Functional Genomics Node (INB-ELIXIR-es). Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, 46012, Spain
| | - H Esteban Hopp
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rainer Hoefgen
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Norma Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Fernández
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Ruth A Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
| |
Collapse
|
10
|
Gonzalez S, Clavijo B, Rivarola M, Moreno P, Fernandez P, Dopazo J, Paniego N. ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. BMC Bioinformatics 2017; 18:121. [PMID: 28222698 PMCID: PMC5320735 DOI: 10.1186/s12859-017-1494-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/21/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species. RESULTS We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results. CONCLUSIONS ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net .
Collapse
Affiliation(s)
- Sergio Gonzalez
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires Argentina
| | | | - Máximo Rivarola
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB Argentina
| | - Patricio Moreno
- Instituto de Ingeniería Biomédica, Facultad de Ingeniería, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula Fernandez
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB Argentina
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires Argentina
| | - Joaquín Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Norma Paniego
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB Argentina
| |
Collapse
|
11
|
López Gialdi AI, Moschen S, Villán CS, López Fernández MP, Maldonado S, Paniego N, Heinz RA, Fernandez P. Identification and characterization of contrasting sunflower genotypes to early leaf senescence process combining molecular and physiological studies (Helianthus annuus L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 250:40-50. [PMID: 27457982 DOI: 10.1016/j.plantsci.2016.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 05/22/2023]
Abstract
Leaf senescence is a complex mechanism ruled by multiple genetic and environmental variables that affect crop yields. It is the last stage in leaf development, is characterized by an active decline in photosynthetic rate, nutrients recycling and cell death. The aim of this work was to identify contrasting sunflower inbred lines differing in leaf senescence and to deepen the study of this process in sunflower. Ten sunflower genotypes, previously selected by physiological analysis from 150 inbred genotypes, were evaluated under field conditions through physiological, cytological and molecular analysis. The physiological measurement allowed the identification of two contrasting senescence inbred lines, R453 and B481-6, with an increase in yield in the senescence delayed genotype. These findings were confirmed by cytological and molecular analysis using TUNEL, genomic DNA gel electrophoresis, flow sorting and gene expression analysis by qPCR. These results allowed the selection of the two most promising contrasting genotypes, which enables future studies and the identification of new biomarkers associated to early senescence in sunflower. In addition, they allowed the tuning of cytological techniques for a non-model species and its integration with molecular variables.
Collapse
Affiliation(s)
- A I López Gialdi
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, 25 de Mayo, San Martín, Buenos Aires, Argentina
| | - S Moschen
- Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y de los Reseros, Hurlingham, Buenos Aires, Argentina
| | - C S Villán
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones. Ruta Nacional 12 Km 7.5, Posadas, Misiones, Argentina
| | - M P López Fernández
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Buenos Aires. Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - S Maldonado
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Buenos Aires. Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - N Paniego
- Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y de los Reseros, Hurlingham, Buenos Aires, Argentina
| | - R A Heinz
- Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y de los Reseros, Hurlingham, Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Buenos Aires. Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - P Fernandez
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, 25 de Mayo, San Martín, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y de los Reseros, Hurlingham, Buenos Aires, Argentina.
| |
Collapse
|
12
|
Raineri J, Hartman MD, Chan RL, Iglesias AA, Ribichich KF. A sunflower WRKY transcription factor stimulates the mobilization of seed-stored reserves during germination and post-germination growth. PLANT CELL REPORTS 2016; 35:1875-90. [PMID: 27251125 DOI: 10.1007/s00299-016-2002-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/24/2016] [Indexed: 05/08/2023]
Abstract
The sunflower transcription factor HaWRKY10 stimulates reserves mobilization in Arabidopsis. Gene expression and enzymes activity assays indicated that lipolysis and gluconeogenesis were increased. Microarray results suggested a parallelism in sunflower. Germinating oilseeds converts stored lipids into sugars, and thereafter in metabolic energy that is used in seedling growth and establishment. During germination, the induced lipolysis linked to the glyoxylate pathway and gluconeogenesis produces sucrose, which is then transported to the embryo and driven through catabolic routes. Herein, we report that the sunflower transcription factor HaWRKY10 regulates carbon partitioning by reducing carbohydrate catabolism and increasing lipolysis and gluconeogenesis. HaWRKY10 was regulated by abscisic acid and gibberellins in the embryo leaves 48 h after seed imbibition and highly expressed during sunflower seed germination and seedling growth, concomitantly with lipid mobilization. Sunflower leaf disks overexpressing HaWRKY10 showed repressed expression of genes related to sucrose cleavage and glycolysis compared with controls. Moreover, HaWRKY10 constitutive expression in Arabidopsis seeds produced higher decrease in lipid reserves, whereas starch and sucrose were more preserved compared with wild type. Gene transcripts abundance and enzyme activities involved in stored lipid mobilization and gluconeogenesis increased more in transgenic than in wild type seeds 36 h after imbibition, whereas the negative regulator of lipid mobilization, ABI4, was repressed. Altogether, the results point out a functional parallelism between tissues and plant species, and reveal HaWRKY10 as a positive regulator of storage reserve mobilization in sunflower.
Collapse
Affiliation(s)
- Jesica Raineri
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional Nº 168 km. 0, Paraje El Pozo (3000), Santa Fe, Argentina
| | - Matías D Hartman
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional Nº 168 km. 0, Paraje El Pozo (3000), Santa Fe, Argentina
| | - Raquel L Chan
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional Nº 168 km. 0, Paraje El Pozo (3000), Santa Fe, Argentina
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional Nº 168 km. 0, Paraje El Pozo (3000), Santa Fe, Argentina
| | - Karina F Ribichich
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional Nº 168 km. 0, Paraje El Pozo (3000), Santa Fe, Argentina.
| |
Collapse
|
13
|
Moschen S, Higgins J, Di Rienzo JA, Heinz RA, Paniego N, Fernandez P. Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower. BMC Bioinformatics 2016; 17 Suppl 5:174. [PMID: 27295368 PMCID: PMC4905614 DOI: 10.1186/s12859-016-1045-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background In recent years, high throughput technologies have led to an increase of datasets from omics disciplines allowing the understanding of the complex regulatory networks associated with biological processes. Leaf senescence is a complex mechanism controlled by multiple genetic and environmental variables, which has a strong impact on crop yield. Transcription factors (TFs) are key proteins in the regulation of gene expression, regulating different signaling pathways; their function is crucial for triggering and/or regulating different aspects of the leaf senescence process. The study of TF interactions and their integration with metabolic profiles under different developmental conditions, especially for a non-model organism such as sunflower, will open new insights into the details of gene regulation of leaf senescence. Results Weighted Gene Correlation Network Analysis (WGCNA) and BioSignature Discoverer (BioSD, Gnosis Data Analysis, Heraklion, Greece) were used to integrate transcriptomic and metabolomic data. WGCNA allowed the detection of 10 metabolites and 13 TFs whereas BioSD allowed the detection of 1 metabolite and 6 TFs as potential biomarkers. The comparative analysis demonstrated that three transcription factors were detected through both methodologies, highlighting them as potentially robust biomarkers associated with leaf senescence in sunflower. Conclusions The complementary use of network and BioSignature Discoverer analysis of transcriptomic and metabolomic data provided a useful tool for identifying candidate genes and metabolites which may have a role during the triggering and development of the leaf senescence process. The WGCNA tool allowed us to design and test a hypothetical network in order to infer relationships across selected transcription factor and metabolite candidate biomarkers involved in leaf senescence, whereas BioSignature Discoverer selected transcripts and metabolites which discriminate between different ages of sunflower plants. The methodology presented here would help to elucidate and predict novel networks and potential biomarkers of leaf senescence in sunflower. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1045-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sebastián Moschen
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Janet Higgins
- The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Julio A Di Rienzo
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Ruth A Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Norma Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Fernandez
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina. .,Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina.
| |
Collapse
|
14
|
Cabello JV, Giacomelli JI, Piattoni CV, Iglesias AA, Chan RL. The sunflower transcription factor HaHB11 improves yield, biomass and tolerance to flooding in transgenic Arabidopsis plants. J Biotechnol 2016; 222:73-83. [PMID: 26876611 DOI: 10.1016/j.jbiotec.2016.02.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/03/2016] [Accepted: 02/08/2016] [Indexed: 11/17/2022]
Abstract
HaHB11 is a member of the sunflower homeodomain-leucine zipper I subfamily of transcription factors. The analysis of a sunflower microarray hybridized with RNA from HaHB11-transformed leaf-disks indicated the regulation of many genes encoding enzymes from glycolisis and fermentative pathways. A 1300bp promoter sequence, fused to the GUS reporter gene, was used to transform Arabidopsis plants showing an induction of expression after flooding treatments, concurrently with HaHB11 regulation by submergence in sunflower. Arabidopsis transgenic plants expressing HaHB11 under the control of the CaMV 35S promoter and its own promoter were obtained and these plants exhibited significant increases in rosette and stem biomass. All the lines produced more seeds than controls and particularly, those of high expression level doubled seeds yield. Transgenic plants also showed tolerance to flooding stress, both to submergence and waterlogging. Carbohydrates contents were higher in the transgenics compared to wild type and decreased less after submergence treatments. Finally, transcript levels of selected genes involved in glycolisis and fermentative pathways as well as the corresponding enzymatic activities were assessed both, in sunflower and transgenic Arabidopsis plants, before and after submergence. Altogether, the present work leads us to propose HaHB11 as a biotechnological tool to improve crops yield, biomass and flooding tolerance.
Collapse
Affiliation(s)
- Julieta V Cabello
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina
| | - Jorge I Giacomelli
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina
| | - Claudia V Piattoni
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina
| | - Raquel L Chan
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina.
| |
Collapse
|
15
|
Moschen S, Bengoa Luoni S, Di Rienzo JA, Caro MDP, Tohge T, Watanabe M, Hollmann J, González S, Rivarola M, García-García F, Dopazo J, Hopp HE, Hoefgen R, Fernie AR, Paniego N, Fernández P, Heinz RA. Integrating transcriptomic and metabolomic analysis to understand natural leaf senescence in sunflower. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:719-34. [PMID: 26132509 DOI: 10.1111/pbi.12422] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 05/12/2015] [Accepted: 05/25/2015] [Indexed: 05/20/2023]
Abstract
Leaf senescence is a complex process, which has dramatic consequences on crop yield. In sunflower, gap between potential and actual yields reveals the economic impact of senescence. Indeed, sunflower plants are incapable of maintaining their green leaf area over sustained periods. This study characterizes the leaf senescence process in sunflower through a systems biology approach integrating transcriptomic and metabolomic analyses: plants being grown under both glasshouse and field conditions. Our results revealed a correspondence between profile changes detected at the molecular, biochemical and physiological level throughout the progression of leaf senescence measured at different plant developmental stages. Early metabolic changes were detected prior to anthesis and before the onset of the first senescence symptoms, with more pronounced changes observed when physiological and molecular variables were assessed under field conditions. During leaf development, photosynthetic activity and cell growth processes decreased, whereas sucrose, fatty acid, nucleotide and amino acid metabolisms increased. Pathways related to nutrient recycling processes were also up-regulated. Members of the NAC, AP2-EREBP, HB, bZIP and MYB transcription factor families showed high expression levels, and their expression level was highly correlated, suggesting their involvement in sunflower senescence. The results of this study thus contribute to the elucidation of the molecular mechanisms involved in the onset and progression of leaf senescence in sunflower leaves as well as to the identification of candidate genes involved in this process.
Collapse
Affiliation(s)
- Sebastián Moschen
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Sofía Bengoa Luoni
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Argentina
| | - Julio A Di Rienzo
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María Del Pilar Caro
- Instituto Superior de Investigaciones Biológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Julien Hollmann
- Institute of Botany, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sergio González
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Máximo Rivarola
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Francisco García-García
- Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe, Valencia, España
- Functional Genomics Node, National Institute of Bioinformatics, Centro de Investigación Príncipe Felipe, Valencia, España
| | - Joaquin Dopazo
- Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe, Valencia, España
- Functional Genomics Node, National Institute of Bioinformatics, Centro de Investigación Príncipe Felipe, Valencia, España
| | - Horacio Esteban Hopp
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rainer Hoefgen
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Norma Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Fernández
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Argentina
| | - Ruth A Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
16
|
Spetale FE, Tapia E, Krsticevic F, Roda F, Bulacio P. A Factor Graph Approach to Automated GO Annotation. PLoS One 2016; 11:e0146986. [PMID: 26771463 PMCID: PMC4714749 DOI: 10.1371/journal.pone.0146986] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/23/2015] [Indexed: 12/19/2022] Open
Abstract
As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum.
Collapse
Affiliation(s)
- Flavio E. Spetale
- CIFASIS-Conicet Institute, Rosario, Argentina
- Facultad de Cs. Exactas, Ingeniería y Agrimensura, National University of Rosario, Rosario, Argentina
| | - Elizabeth Tapia
- CIFASIS-Conicet Institute, Rosario, Argentina
- Facultad de Cs. Exactas, Ingeniería y Agrimensura, National University of Rosario, Rosario, Argentina
| | - Flavia Krsticevic
- CIFASIS-Conicet Institute, Rosario, Argentina
- Facultad Regional San Nicolás, National Technological University, San Nicolás, Argentina
| | | | - Pilar Bulacio
- CIFASIS-Conicet Institute, Rosario, Argentina
- Facultad de Cs. Exactas, Ingeniería y Agrimensura, National University of Rosario, Rosario, Argentina
- Facultad Regional San Nicolás, National Technological University, San Nicolás, Argentina
| |
Collapse
|
17
|
Wang J, Yang X, Xiao H, Kong J, Bing M. Determination of the mechanism of action of repetitive halothane exposure on rat brain tissues using a combined method of microarray gene expression profiling and bioinformatics analysis. Mol Med Rep 2015; 12:8071-6. [PMID: 26497548 DOI: 10.3892/mmr.2015.4462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 04/15/2015] [Indexed: 11/05/2022] Open
Abstract
The present study aimed to investigate the gene expression profiles of rats brain tissues treated with halothane compared with untreated controls to improve current understanding of the mechanism of action of the inhaled anesthetic. The GSE357 gene expression profile was dowloaded from the Gene Expression Omnibus database, and included six gene chips of samples repeatedly exposed to halothane and 12 gene chips of untreated controls. The differentially expressed genes (DEGs) between these two groups were identified using the Limma package in R language. Subsequently, the Database for Annotation, Visualization and Integrated Discovery was used to annotate the function of these DEGs. In addition, the most significantly upregulated gene and downregulated gene were annotated, to reveal the functional interactions with other associated genes, in FuncBase database. A total of 44 DEGs were obtained between The control and halothane exposure samples. Following Gene Ontology functional classification, these DEGs were found to be involved predominantly in the circulatory system, regulation of cell proliferation and response to endogenous stimulus and corticosteroid stimulus processes. KRT31 and HMGCS2, which were identified as the most significantly downregulated and upregulated DEGs, respectively, were associated with the lipid metabolic process and T cell activation, respectively. These results provided a basis for the development of improved inhalational anesthetics with minimal side effects and are essential for optimization of inhaled anesthetic techniques for advanced surgical procedures.
Collapse
Affiliation(s)
- Jiansheng Wang
- Department of Anesthesiology, Shanghai Baoshan District Integrated Traditional and Western Medicine Hospital, Shanghai 201900, P.R. China
| | - Xiaojun Yang
- Department of Anesthesiology, Shanghai Baoshan District Integrated Traditional and Western Medicine Hospital, Shanghai 201900, P.R. China
| | - Huan Xiao
- Department of Anesthesiology, Shanghai Baoshan District Integrated Traditional and Western Medicine Hospital, Shanghai 201900, P.R. China
| | - Jianqiang Kong
- Department of Anesthesiology, Shanghai Baoshan District Integrated Traditional and Western Medicine Hospital, Shanghai 201900, P.R. China
| | - Miao Bing
- Department of Anesthesiology, Shanghai Baoshan District Integrated Traditional and Western Medicine Hospital, Shanghai 201900, P.R. China
| |
Collapse
|
18
|
Pinedo M, Orts F, Carvalho ADO, Regente M, Soares JR, Gomes VM, de la Canal L. Molecular characterization of Helja, an extracellular jacalin-related protein from Helianthus annuus: Insights into the relationship of this protein with unconventionally secreted lectins. JOURNAL OF PLANT PHYSIOLOGY 2015; 183:144-53. [PMID: 26140981 DOI: 10.1016/j.jplph.2015.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 05/21/2015] [Accepted: 06/11/2015] [Indexed: 05/25/2023]
Abstract
Jacalin-related lectins (JRLs) encompass cytosolic, nuclear and vacuolar members displaying the jacalin domain in one or more copies or in combination with unrelated domains. Helianthus annuus jacalin (Helja) is a mannose-specific JRL previously identified in the apoplast of Helianthus annuus seedlings, and this protein has been proposed to follow unconventional secretion. Here, we describe the full-length Helja cDNA sequence, which presents a unique jacalin domain (merolectin) and the absence of a signal peptide, confirming that the protein cannot follow the classical ER-dependent secretory pathway. Helja mRNA is present in seeds, cotyledons, roots and hypocotyls, but no transcripts were detected in the leaves. Searches for sequence similarity showed that Helja is barely similar to other JRLs present in H. annuus databases and less than 45% identical to other monocot or dicot JRLs. Strikingly, most of the merolectins recovered through data mining using Helja as a query were predicted as apoplastic, although most of these proteins lack the signal peptide required for classical secretion. Thus, Helja is the first bait identified to recover putative unconventionally secreted lectins. Because the recovered JRLs are widely distributed among the plant kingdom, an as yet unknown role for jacalin lectins in the apoplast is emerging.
Collapse
Affiliation(s)
- Marcela Pinedo
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Funes 3250, 7600 Mar del Plata, Argentina.
| | - Facundo Orts
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Funes 3250, 7600 Mar del Plata, Argentina.
| | - André de Oliveira Carvalho
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes 28013-602, RJ, Brazil.
| | - Mariana Regente
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Funes 3250, 7600 Mar del Plata, Argentina.
| | - Julia Ribeiro Soares
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Funes 3250, 7600 Mar del Plata, Argentina.
| | - Valdirene Moreira Gomes
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes 28013-602, RJ, Brazil.
| | - Laura de la Canal
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Funes 3250, 7600 Mar del Plata, Argentina.
| |
Collapse
|
19
|
Jung WY, Lee SS, Kim CW, Kim HS, Min SR, Moon JS, Kwon SY, Jeon JH, Cho HS. RNA-seq analysis and de novo transcriptome assembly of Jerusalem artichoke (Helianthus tuberosus Linne). PLoS One 2014; 9:e111982. [PMID: 25375764 PMCID: PMC4222968 DOI: 10.1371/journal.pone.0111982] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 10/09/2014] [Indexed: 11/18/2022] Open
Abstract
Jerusalem artichoke (Helianthus tuberosus L.) has long been cultivated as a vegetable and as a source of fructans (inulin) for pharmaceutical applications in diabetes and obesity prevention. However, transcriptomic and genomic data for Jerusalem artichoke remain scarce. In this study, Illumina RNA sequencing (RNA-Seq) was performed on samples from Jerusalem artichoke leaves, roots, stems and two different tuber tissues (early and late tuber development). Data were used for de novo assembly and characterization of the transcriptome. In total 206,215,632 paired-end reads were generated. These were assembled into 66,322 loci with 272,548 transcripts. Loci were annotated by querying against the NCBI non-redundant, Phytozome and UniProt databases, and 40,215 loci were homologous to existing database sequences. Gene Ontology terms were assigned to 19,848 loci, 15,434 loci were matched to 25 Clusters of Eukaryotic Orthologous Groups classifications, and 11,844 loci were classified into 142 Kyoto Encyclopedia of Genes and Genomes pathways. The assembled loci also contained 10,778 potential simple sequence repeats. The newly assembled transcriptome was used to identify loci with tissue-specific differential expression patterns. In total, 670 loci exhibited tissue-specific expression, and a subset of these were confirmed using RT-PCR and qRT-PCR. Gene expression related to inulin biosynthesis in tuber tissue was also investigated. Exsiting genetic and genomic data for H. tuberosus are scarce. The sequence resources developed in this study will enable the analysis of thousands of transcripts and will thus accelerate marker-assisted breeding studies and studies of inulin biosynthesis in Jerusalem artichoke.
Collapse
Affiliation(s)
- Won Yong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea; Animal Material Engineering, Gyeongnam National University of Science and Technology, Jinju, Korea
| | - Sang Sook Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Chul Wook Kim
- Animal Material Engineering, Gyeongnam National University of Science and Technology, Jinju, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sung Ran Min
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jae Sun Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| |
Collapse
|
20
|
Moschen S, Bengoa Luoni S, Paniego NB, Hopp HE, Dosio GAA, Fernandez P, Heinz RA. Identification of candidate genes associated with leaf senescence in cultivated sunflower (Helianthus annuus L.). PLoS One 2014; 9:e104379. [PMID: 25110882 PMCID: PMC4128711 DOI: 10.1371/journal.pone.0104379] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 07/13/2014] [Indexed: 11/18/2022] Open
Abstract
Cultivated sunflower (Helianthus annuus L.), an important source of edible vegetable oil, shows rapid onset of senescence, which limits production by reducing photosynthetic capacity under specific growing conditions. Carbon for grain filling depends strongly on light interception by green leaf area, which diminishes during grain filling due to leaf senescence. Transcription factors (TFs) regulate the progression of leaf senescence in plants and have been well explored in model systems, but information for many agronomic crops remains limited. Here, we characterize the expression profiles of a set of putative senescence associated genes (SAGs) identified by a candidate gene approach and sunflower microarray expression studies. We examined a time course of sunflower leaves undergoing natural senescence and used quantitative PCR (qPCR) to measure the expression of 11 candidate genes representing the NAC, WRKY, MYB and NF-Y TF families. In addition, we measured physiological parameters such as chlorophyll, total soluble sugars and nitrogen content. The expression of Ha-NAC01, Ha-NAC03, Ha-NAC04, Ha-NAC05 and Ha-MYB01 TFs increased before the remobilization rate increased and therefore, before the appearance of the first physiological symptoms of senescence, whereas Ha-NAC02 expression decreased. In addition, we also examined the trifurcate feed-forward pathway (involving ORE1, miR164, and ethylene insensitive 2) previously reported for Arabidopsis. We measured transcription of Ha-NAC01 (the sunflower homolog of ORE1) and Ha-EIN2, along with the levels of miR164, in two leaves from different stem positions, and identified differences in transcription between basal and upper leaves. Interestingly, Ha-NAC01 and Ha-EIN2 transcription profiles showed an earlier up-regulation in upper leaves of plants close to maturity, compared with basal leaves of plants at pre-anthesis stages. These results suggest that the H. annuus TFs characterized in this work could play important roles as potential triggers of leaf senescence and thus can be considered putative candidate genes for senescence in sunflower.
Collapse
Affiliation(s)
- Sebastian Moschen
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Sofia Bengoa Luoni
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Norma B. Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - H. Esteban Hopp
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Guillermo A. A. Dosio
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Fisiología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Paula Fernandez
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Ruth A. Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
| |
Collapse
|
21
|
Corti Monzón G, Pinedo M, Di Rienzo J, Novo-Uzal E, Pomar F, Lamattina L, de la Canal L. Nitric oxide is required for determining root architecture and lignin composition in sunflower. Supporting evidence from microarray analyses. Nitric Oxide 2014; 39:20-8. [PMID: 24747108 DOI: 10.1016/j.niox.2014.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 04/01/2014] [Accepted: 04/07/2014] [Indexed: 01/09/2023]
Abstract
Nitric oxide (NO) is a signal molecule involved in several physiological processes in plants, including root development. Despite the importance of NO as a root growth regulator, the knowledge about the genes and metabolic pathways modulated by NO in this process is still limited. A constraint to unravel these pathways has been the use of exogenous applications of NO donors that may produce toxic effects. We have analyzed the role of NO in root architecture through the depletion of endogenous NO using the scavenger cPTIO. Sunflower seedlings growing in liquid medium supplemented with cPTIO showed unaltered primary root length while the number of lateral roots was deeply reduced; indicating that endogenous NO participates in determining root branching in sunflower. The transcriptional changes induced by NO depletion have been analyzed using a large-scale approach. A microarray analysis showed 330 genes regulated in the roots (p≤0.001) upon endogenous NO depletion. A general cPTIO-induced up-regulation of genes involved in the lignin biosynthetic pathway was observed. Even if no detectable changes in total lignin content could be detected, cell walls analyses revealed that the ratio G/S lignin increased in roots treated with cPTIO. This means that endogenous NO may control lignin composition in planta. Our results suggest that a fine tuning regulation of NO levels could be used by plants to regulate root architecture and lignin composition. The functional implications of these findings are discussed.
Collapse
Affiliation(s)
- Georgina Corti Monzón
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Mar del Plata, Argentina.
| | - Marcela Pinedo
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Mar del Plata, Argentina.
| | - Julio Di Rienzo
- Cátedra de Estadística y Biometría, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina.
| | - Esther Novo-Uzal
- Departamento de Biología Vegetal, Universidad de Murcia, Murcia, Spain.
| | - Federico Pomar
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidade da Coruña, A Coruña, Spain.
| | - Lorenzo Lamattina
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Mar del Plata, Argentina.
| | - Laura de la Canal
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata-CONICET, Mar del Plata, Argentina.
| |
Collapse
|
22
|
Kawakami T, Darby BJ, Ungerer MC. Transcriptome resources for the perennial sunflowerHelianthus maximilianiobtained from ecologically divergent populations. Mol Ecol Resour 2014; 14:812-9. [DOI: 10.1111/1755-0998.12227] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/07/2014] [Accepted: 01/08/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Takeshi Kawakami
- Division of Biology; Kansas State University; Manhattan KS 66506 USA
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Brian J. Darby
- Department of Biology; University of North Dakota; Grand Forks ND 58202 USA
| | - Mark C. Ungerer
- Division of Biology; Kansas State University; Manhattan KS 66506 USA
| |
Collapse
|
23
|
Kim KU, Park SK, Kang SA, Park MK, Cho MK, Jung HJ, Kim KY, Yu HS. Comparison of functional gene annotation of Toxascaris leonina and Toxocara canis using CLC genomics workbench. THE KOREAN JOURNAL OF PARASITOLOGY 2013; 51:525-30. [PMID: 24327777 PMCID: PMC3857499 DOI: 10.3347/kjp.2013.51.5.525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Revised: 07/23/2013] [Accepted: 08/09/2013] [Indexed: 12/24/2022]
Abstract
The ascarids, Toxocara canis and Toxascaris leonina, are probably the most common gastrointestinal helminths encountered in dogs. In order to understand biological differences of 2 ascarids, we analyzed gene expression profiles of female adults of T. canis and T. leonina using CLC Genomics Workbench, and the results were compared with those of free-living nematode Caenorhabditis elegans. A total of 2,880 and 7,949 ESTs were collected from T. leonina and T. canis, respectively. The length of ESTs ranged from 106 to 4,637 bp with an average insert size of 820 bp. Overall, our results showed that most functional gene annotations of 2 ascarids were quite similar to each other in 3 major categories, i.e., cellular component, biological process, and molecular function. Although some different transcript expression categories were found, the distance was short and it was not enough to explain their different lifestyles. However, we found distinguished transcript differences between ascarid parasites and free-living nematodes. Understanding evolutionary genetic changes might be helpful for studies of the lifestyle and evolution of parasites.
Collapse
Affiliation(s)
- Ki Uk Kim
- Department of Internal Medicine, School of Medicine, Pusan National University, Yangsan 626-870, Korea
| | | | | | | | | | | | | | | |
Collapse
|