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Добірка наукової літератури з теми ""NAC transcription factors""

Автор: Grafiati

Опубліковано: 11 березня 2023

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Статті в журналах з теми ""NAC transcription factors""

Welner, Ditte H., Søren Lindemose, J. Günter Grossmann, Niels Erik Møllegaard, Addie N. Olsen, Charlotte Helgstrand, Karen Skriver, and Leila Lo Leggio. "DNA binding by the plant-specific NAC transcription factors in crystal and solution: a firm link to WRKY and GCM transcription factors." Biochemical Journal 444, no. 3 (May 29, 2012): 395–404. http://dx.doi.org/10.1042/bj20111742.

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NAC (NAM/ATAF/CUC) plant transcription factors regulate essential processes in development, stress responses and nutrient distribution in important crop and model plants (rice, Populus, Arabidopsis), which makes them highly relevant in the context of crop optimization and bioenergy production. The structure of the DNA-binding NAC domain of ANAC019 has previously been determined by X-ray crystallography, revealing a dimeric and predominantly β-fold structure, but the mode of binding to cognate DNA has remained elusive. In the present study, information from low resolution X-ray structures and small angle X-ray scattering on complexes with oligonucleotides, mutagenesis and (DNase I and uranyl photo-) footprinting, is combined to form a structural view of DNA-binding, and for the first time provide experimental evidence for the speculated relationship between plant-specific NAC proteins, WRKY transcription factors and the mammalian GCM (Glial cell missing) transcription factors, which all use a β-strand motif for DNA-binding. The structure shows that the NAC domain inserts the edge of its core β-sheet into the major groove, while leaving the DNA largely undistorted. The structure of the NAC–DNA complex and a new crystal form of the unbound NAC also indicate limited flexibility of the NAC dimer arrangement, which could be important in recognizing suboptimal binding sites.

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Zhao, Shuping, Tao Jiang, Yao Zhang, Kailing Zhang, Kai Feng, Peng Wu, and Liangjun Li. "Identification of the NAC Transcription Factors and Their Function in ABA and Salinity Response in Nelumbo nucifera." International Journal of Molecular Sciences 23, no. 20 (October 16, 2022): 12394. http://dx.doi.org/10.3390/ijms232012394.

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Nelumbo nucifera Gaertn. is an important perennial aquatic herb that has high ornamental, edible, medicinal, and economic value, being widely distributed and used in China. The NAC superfamily (NAM, ATAF1/2, CUC2) plays critical roles in plant growth, development, and response to abiotic and biotic stresses. Though there have been a few reports about NAC genes in lotus, systematic analysis is still relatively lacking. The present study aimed to characterize all the NAC genes in the lotus and obtain better insights on the NnNACs in response to salt stress by depending on ABA signaling. Here, 97 NAC genes were identified by searching the whole lotus genome based on the raw HMM models of the conserved NAM domain and NAC domain. They were characterized by bioinformatics analysis and divided into 18 subgroups based on the phylogenetic tree. Cis-element analysis demonstrated that NAC genes are responsive to biotic and abiotic stresses, light, low temperature, and plant hormones. Meanwhile, NAC genes had tissue expression specificity. qRT-PCR analysis indicated that NAC genes could be upregulated or downregulated by NaCl treatment, ABA, and fluoridone. In addition, NAC016, NAC025, and NAC070, whose encoding genes were significantly induced by NaCl and ABA, were located in the nucleus. Further analysis showed the three NAC proteins had transcriptional activation capabilities. The co-expression network analysis reflected that NAC proteins may form complexes with other proteins to play a role together. Our study provides a theoretical basis for further research to be conducted on the regulatory mechanisms of salinity resistance in the lotus.

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Olsen, Addie Nina, Heidi A. Ernst, Leila Lo Leggio, and Karen Skriver. "NAC transcription factors: structurally distinct, functionally diverse." Trends in Plant Science 10, no. 2 (February 2005): 79–87. http://dx.doi.org/10.1016/j.tplants.2004.12.010.

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Ma, Jianhui, Meng Yuan, Bo Sun, Daijing Zhang, Jie Zhang, Chunxi Li, Yun Shao, Wei Liu, and Lina Jiang. "Evolutionary Divergence and Biased Expression of NAC Transcription Factors in Hexaploid Bread Wheat (Triticum aestivum L.)." Plants 10, no. 2 (February 17, 2021): 382. http://dx.doi.org/10.3390/plants10020382.

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The NAC genes, a large plant-specific family of transcription factors, regulate a wide range of pathways involved in development and response to biotic and abiotic stress. In this study, the NAC transcription factors were identified in 27 green plants, and the results showed that NAC transcription factors in plants undergo an appearance stage from water to land and a number expansion stage from gymnosperm to angiosperm. Investigating the evolutionary process of the NAC transcription factors from diploid species to hexaploid wheat revealed that tandem replications during the polyploidization process is an important event for increasing the number of NAC transcription factors in wheat. Then, the molecular characteristics, phylogenetic relationships, and expression patterns of 462 NAC transcription factors of hexaploid wheat (TaNACs) were analyzed. The protein structure results showed that TaNAC was relatively conservative at the N-terminal that contains five subdomains. All these TaNACs were divided into Group I and Group II by phylogenetic analysis, and the TaNACs in Group I should undergo strong artificial selection based on single nucleotide polymorphism (SNP) analysis. Through genome synteny and phylogenetic analysis, these TaNACs were classified into 88 groups and 9 clusters. The biased expression results of these TaNACs showed that there are 24 groups and 67 groups of neofunctionalization genes under biotic and abiotic stress, respectively, and 16 groups and 59 groups of subfunctionalization genes. This shows that neofunctionalization plays an important role in coping with different stresses. Our study provides new insights into the evolution of NAC transcription factors in hexaploid wheat.

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O’Shea, Charlotte, Mikael Kryger, Emil G. P. Stender, Birthe B. Kragelund, Martin Willemoës, and Karen Skriver. "Protein intrinsic disorder in Arabidopsis NAC transcription factors: transcriptional activation by ANAC013 and ANAC046 and their interactions with RCD1." Biochemical Journal 465, no. 2 (January 6, 2015): 281–94. http://dx.doi.org/10.1042/bj20141045.

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The regulatory domains of NAC [no apical meristem, ATAF (Arabidopsis transcription activation factor), cup-shaped cotyledon] transcription factors (TFs) are mostly disordered. The single molecular recognition feature (MoRF) in ANAC046 (Arabidopsis NAC domain containing protein 46) is a functional hot spot mediating interactions with RCD1 (radical-induced cell death 1), a stress-associated hub which exploits disorder and different mechanisms for interactions.

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Marques, Deyvid N., Sávio P. dos Reis, and Cláudia R. B. de Souza. "Plant NAC transcription factors responsive to abiotic stresses." Plant Gene 11 (September 2017): 170–79. http://dx.doi.org/10.1016/j.plgene.2017.06.003.

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Nakashima, Kazuo, Hironori Takasaki, Junya Mizoi, Kazuo Shinozaki, and Kazuko Yamaguchi-Shinozaki. "NAC transcription factors in plant abiotic stress responses." Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1819, no. 2 (February 2012): 97–103. http://dx.doi.org/10.1016/j.bbagrm.2011.10.005.

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Al-Sayaydeh, Rabea, Khaled Al-Habahbeh, Zahera Akkeh, and Randa N. Albdaiwi. "IN SILICO GENE EXPRESSION ANALYSIS OF THE STRESS-RELATED NAC-A GENE SUBFAMILY TO DISSECT THEIR ROLE IN ABIOTIC STRESS TOLERANCE IN BREAD WHEAT (TRITICUM AESTIVUM L.)." Jordan Journal of Agricultural Sciences 17, no. 3 (September 1, 2021): 341–54. http://dx.doi.org/10.35516/jjas.v17i3.90.

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Wheat is a major staple crop that is largely affected by different abiotic stresses that include heat, drought, and salinity. The main objective of this study was to identify wheat NAC transcription factors that are related to the NAC-a subfamily, which is involved in mediating stress tolerance in different plant species. Furthermore, in silico gene expression analysis was conducted to detect differential changes in wheat NAC-a subfamily members in different organs, developmental stages, and under various abiotic stress. Herein, using phylogenetic analysis for 488 NAC transcription factors, 41 proteins were identified as wheat NAC-a subfamily members. In silico gene expression analysis found that NAC-related wheat transcription factors are expressed exclusively at the anthesis stage till dough development with high expression levels detected in flag leaves. The in-silico gene expression analysis identified SNAC1-related members, which had high expression levels under drought, cold, and heat stresses. The identified stress-induced wheat NAC-a subfamily members can be utilized in the future to develop climate-smart wheat cultivars with improved tolerance against abiotic stresses.

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Toth, Z., E. Kiss, and L. Kovacs. "NAC TRANSCRIPTION FACTORS AS KEY REGULATORS IN STRESS RESPONSES." Acta Horticulturae, no. 1082 (April 2015): 293–98. http://dx.doi.org/10.17660/actahortic.2015.1082.40.

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Christianson, Jed A., Elizabeth S. Dennis, Danny J. Llewellyn, and Iain W. Wilson. "ATAF NAC transcription factors: Regulators of plant stress signaling." Plant Signaling & Behavior 5, no. 4 (April 2010): 428–32. http://dx.doi.org/10.4161/psb.5.4.10847.

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Більше джерел

Дисертації з теми ""NAC transcription factors""

Shelton, Jarod Ross. "CHARACTERIZING THE ROLE OF THE TRANSCRIPTION FACTORS, αNAC, BTF3 AND SKNAC, IN MYOGENESIS". OpenSIUC, 2013. https://opensiuc.lib.siu.edu/theses/1325.

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Myogenesis is a complex and tightly regulated process, the end result of which is the formation of multinucleated myofibers. Muscle formation requires the precise expression of multiple myogenic regulatory factors (MRFs), whose expression regulates transcription of muscle specific proteins. Alteration in the expression of a muscle specific gene or protein ultimately results in muscle dysfunction. The inappropriate expression of factors that control muscle development may also be a contributing factor in Rhabdomyosarcoma, a pediatric cancer that accounts for most soft tissue sarcomas that arise in children. Previous studies suggest that the regulation of αNAC, BTF3, and skNAC are vital for normal myogenesis. Alterations in these factors results in retarded development and severe disorganization of muscle tissue. We hypothesized that αNAC, BTF3, and skNAC are imperative transcription factors whose dysregulation significantly alters the kinetics of C2C12 cell (murine skeletal muscle cells) myogenesis. We have shown that erroneous expression of these transcription factors is detrimental to myogenesis. In addition, we have shown that these transcription factors are recruited to muscle specific gene promoters during the myogenic differentiation program and the expression of αNAC, BTF3, and skNAC may potentiate the expression of the MRFs. Together, our experiments suggest that the expression of αNAC, BTF3, and skNAC are essential for the normal progression of myogenesis.

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Baloglu, Mehmet Cengiz. "Expression Analysis Of Nac Type Transcription Factors On Wheat Seedlings Under Abiotic Stress Conditions." Phd thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12613501/index.pdf.

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Wheat is the most important grain crop grown in our country providing greatest part of the daily nutritional requirement. Abiotic factors including salinity, drought, cold and heat stresses affect quality and yield of wheat varieties used for the production of both bread and pasta flour. NAC proteins form one of the widest families of plant specific transcription factors. Members of this family are related with development, defense and abiotic stress responses. TaNAC69-1 and TtNAM-B2 genes were isolated from T.aestivum and T.turgidum, respectively. Then they were cloned into different monocot and dicot expression vectors to be used for further wheat and tobacco genetic transformation studies. To understand effects of salinity, drought, cold and heat stresses on expression profiles of TaNAC69-1 and TtNAM-B2 genes, quantitative real time PCR was performed. The time series expression profiles of TaNAC69-1 show that it was signi

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FORLANI, SARA. "INVESTIGATING PLANT SENESCENCE: THE ROLE OF NAC TRANSCRIPTION FACTORS IN SOLANUM LYCOPERSICUM AND ARABIDOPSIS THALIANA." Doctoral thesis, Università degli Studi di Milano, 2021. http://hdl.handle.net/2434/849040.

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THESIS OUTLINE In the present thesis work, the senescence process in fruit and leaf has been investigated through the analysis of different mutant lines of Arabidopsis thaliana and Solanum lycopersicum. In particular, the work has focused on the downregulation of three NAC transcription factor genes, NAC058 (AT3G18400), NAC100 (AT5G61430, both analysed in Arabidopsis), and HEBE (Solyc12g036480), analysed in tomato. All of them have been selected for the analysis due to their putative role in senescence, e.g. their expression has been detected in senescing siliques (NAC058, NAC100) and in ripening berries (NAC100). In addition, HEBE is the putative ortholog in tomato of NAC058 of Arabidopsis. The work has been divided in the following chapters: - CHARACTERIZATION OF NAC058, A NEGATIVE SENESCENCE REGULATOR IN SILIQUES OF Arabidopsis thaliana - in this section, NAC058 is identified as fruit-specific negative regulator of senescence. Overexpression lines are analysed and NAC058 expression is localized in different tissues of 21 the siliques. Moreover, the bond between this transcription factor and phytohormones is preliminarly evaluated. - NAC100, A NOVEL NAC TRANSCRIPTION FACTOR THAT NEGATIVELY REGULATES FRUIT SENESCENCE IN Arabidopsis thaliana – in this chapter, a comparison between transcriptomic data of Arabidopsis senescing siliques and tomato ripening berries allows to identify conserved NAC genes expressed during fruit maturation. 7 Arabidopsis lines carrying T-DNA insertions in these genes are analysed looking at senescence-related traits and, among them, nac100 is selected as putative negative regulator of silique senescence. In addition, NAC100 is found to affect silique development. - HEBE, A NOVEL POSITIVE REGULATOR OF LEAF SENESCENCE IN Solanum lycopersicum – in this section, HEBE, the putative ortholog of NAC058 in tomato, is temporary silenced in tomato plants through Virus-Induced Gene Silencing (VIGS), resulting in a stay-green phenotype. The work has been published in 2020 (paper in attachment at the chapter).

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Guérin, Claire. "Analyse des facteurs de transcription de la famille NAC chez le blé tendre (Triticum aestivum L.) et leur implication dans la réponse à des stress abiotiques." Thesis, Université Clermont Auvergne‎ (2017-2020), 2019. http://www.theses.fr/2019CLFAC014/document.

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Le blé tendre, Triticum aestivum, est une des céréales les plus cultivées dans le monde. Le changement climatique qui se développe actuellement contraint fortement les cultures et altère leur rendement. La compréhension des mécanismes de réponse du blé tendre aux stress abiotiques est donc une problématique d’actualité. Plusieurs grandes familles de facteurs de transcription, dont la famille NAC,interviennent dans le développement de la plante et dans sa réponse aux stress environnementaux. Cette thèse, structurée en 3 volets, est ciblée sur l’étude de la famille NAC chez le blé tendre : les TaNAC. Dans un premier temps, nous avons étudié la structuration génomique et phylogénétique des 488 membres de la famille TaNAC, recensés à partir de la base de données la plus récente du blé tendre.Nous avons aussi étudié l’histoire évolutive de cette famille, qui a été marquée par des événements de duplication et de rétroposition. Enfin, une analyse de sa diversité allélique a permis d’identifier des gènes qui présentent des SNP montrant une forte association avec des paramètres d’accumulation des protéines de réserve dans le grain. Le deuxième chapitre de cette thèse a porté sur l’étude de l’expression de ces 488 gènes TaNAC dans plusieurs organes et en réponse aux stress thermique et sécheresse. Une analyse globale a été réalisée à partir de données bio-informatiques, suivie d’une étude in planta de l’expression d’une sélection de 23 gènes. Les profils d’expression obtenus ont révélé l’existence de 4 gènes TaNAC, encore jamais décrits dans la littérature et qui interviennent dans le développement du grain de blé tendre mais aussi dans sa réponse adaptative à plusieurs stress abiotiques. Le troisième volet de cette thèse a donc porté sur la caractérisation génétique, moléculaire et physiologique de ces 4 facteurs de transcription TaNAC. Ils appartiennent à un clade rassemblant des séquences présentant des similitudes génomique et structurale. De plus, ils sont localisés dans le noyau et leurs profils d’expression sont similaires, avec toutefois un niveau variable entre gènes et entre homéologues pour chaque gène. En réponse à un stress thermique modéré, ce profil d’expression est accéléré au cours du développement du grain ; le stade 120°Cj étant le stade clé qui montre la plus grande différence d’expression de ces gènes entre les conditions contrôle et stressée. Pour des raisons techniques, la production de plantes transgéniques sur- et sous-exprimant ces gènes n’a pas permis de valider l’implication de ces 4 TaNAC dans le développement du grain et en réponse à la température. Une analyse de génétique d’association a toutefois permis de mettre en évidence un lien entre des marqueurs moléculaires situés dans ces gènes et l’accumulation des protéines de réserve.Globalement, les résultats obtenus ont montré que des membres de la famille TaNAC sont impliqués dans le développement du blé tendre et dans sa réponse aux stress abiotiques. Plus particulièrement, 4 facteurs de transcription TaNAC semblent jouer un rôle clé dans l’accumulation des protéines dans le grain en réponse à un stress thermique modéré
Bread wheat, Triticum aestivum, is one of the most cultivated cereal in the world. The climate change that is currently developing strongly constrains crops and impairs their yield. Understanding the wheat response mechanisms to abiotic stresses is therefore a current issue. Several major families of transcription factors, including the NAC family, are involved in the plant development and its response to environmental stresses. This thesis, structured in three parts, is focused on the study of the NAC family in bread wheat (TaNAC).First, we studied the genomic and phylogenetic structure of the 488 members of the TaNAC family identified from the latest database of bread wheat. We also studied the evolutionary history of this family, which was marked by duplication and retroposition events. Finally, an analysis of its allelic diversity allows us to identify genes with SNP showing a strong association with storage protein accumulation parameters in the grain. In a second part, we studied the expression of these 488 TaNAC genes in several organs and in response to heat and drought. An overall analysis was performed using bioinformatic data, followed by an in planta study of the expression of a selection of 23 genes. The expression profiles revealed that four TaNAC genes, never described in the literature, are involved in the wheat grain development but also in its adaptive response to several abiotic stresses. In a third part, we focused on the genetic, molecular and physiological characterization of these four TaNAC transcription factors. They belong to a clade gathering sequences with genomic and structural similarities. Moreover, they are localized in the nucleus and their expression profiles are similar, with a variable level between genes and between homeologs for each gene. In response to moderate heat stress, this expression profile is accelerated during grain development and a key stage at 120°Cj was identified, it shows the greatest difference in genes expression level between control and stressed conditions. For technical reasons, the production of transgenic plants over- and under-expressing these genes did not validate the involvement of these 4 TaNAC in grain development and in its temperature response. An association genetic analysis, however, showed a link between molecular markers located in these genes and the storage proteins accumulation. Overall, the results showed that members of the TaNAC family are involved in the bread wheat development and its response to abiotic stresses. In particular, four TaNAC transcription factors appear to play a key role in grain protein accumulation in response to a moderate heat stress

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Grant, Emily H. "Functional characterization of NAC-domain transcription factors implicated in control of vascular cell differentiation in Arabidopsis and Populus." Thesis, Virginia Tech, 2008. http://hdl.handle.net/10919/36373.

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Wood has a wide variety of uses and is arguably the most important renewable raw material. The composition of xylem cell types in wood determines the utility of different types of wood for distinct commercial applications. Using expression profiling and phylogenetic analysis, we identified many xylem-associated regulatory genes that may control the differentiation of cells involved in wood formation in Arabidopsis and poplar. Prominent among these are NAC-domain transcription factors (NACs). In addition to their roles as regulators of xylem differentiation, NACs are regulators of meristem development, organ elongation and separation. We studied a subset of Populus and Arabidopsis NACs with putative involvement in xylem cell expansion and elongation (XND1/ANAC104, PopNAC118, PopNAC122, PopNAC128, PopNAC129), and secondary cell wall synthesis (ANAC073, PopNAC105, PopNAC154, PopNAC156, PopNAC157). Using quantitative Real-Time PCR, we evaluated expression of the selected Populus NACs in a developmental gradient and in response to bending stress. We prepared transgenic Arabidopsis and Populus plants with increased or decreased expression of select NAC genes. For dominant repression of target gene expression, we evaluated transgenic plants expressing translational fusions of NAC-EAR (ERF amphiphilic repressor) chimeras through chimeric repressor silencing-technology (CRES-T). XND1 overexpression in Populus and Arabidopsis resulted in severe stunting and suppression of xylem differentiation. Overexpression of PopNAC122, an XND1 ortholog, yielded an analogous phenotype in Arabidopsis. Populus XND1 overexpressors lacked phloem fibers and showed a reduction in cell size and number, vessel number and frequency of rays. Knowledge gained through characterization of these wood-associated regulatory genes can be used to optimize molecular breeding and genetic engineering strategies for improved wood quality and increased biomass.
Master of Science

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Ratnakaran, Neena [Verfasser], Christiane [Akademischer Betreuer] Gatz, and Volker [Akademischer Betreuer] Lipka. "Identification of the role of Arabidopsis ATAF-type NAC transcription factors in plant stress and development / Neena Ratnakaran. Gutachter: Christiane Gatz ; Volker Lipka. Betreuer: Christiane Gatz." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2014. http://d-nb.info/1051132711/34.

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Wang, Bo. "Transcriptional regulation of the human NAD(P)H: quinone oxidoreductase gene during oxidative stress." Thesis, University of East Anglia, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.262435.

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Hussey, Steven Grant. "Functional genomics of NAC transcription factor SND2 regulating secondary cell wall biosynthesis in Arabidopsis and Eucalyptus." Thesis, University of Pretoria, 2014. http://hdl.handle.net/2263/79245.

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Wood formation is heavily exploited for the manufacturing of pulp, paper, sustainable biomaterials and, potentially, biofuels. Eucalyptus is a favourable fast-growing, short rotation plantation crop grown over millions of hectares globally for its superior fiber properties. Understanding the molecular biology of secondary cell wall (SCW) formation in trees, and in particular how it is transcriptionally and epigenetically regulated, lays the foundation for enhanced woody trait improvement strategies in tree biotechnology. Transcriptional networks regulating SCW biosynthesis have been discovered in the herbaceous model plant Arabidopsis thaliana, in which NAC domain transcription factors (TFs) play a prominent role. The functions of many NAC domain TFs remain to be resolved, and their regulatory roles and evolution in Eucalyptus is unknown. Functional genomics studies of Eucalyptus TFs are currently challenged by a lack of established high-throughput genomics techniques commonly applied to model organisms. In this study, we aimed to better understand NAC family evolution and the epigenetic regulation of xylogenesis in E. grandis, and characterize the role of NAC domain TF SND2 in transcriptional regulation of SCW biosynthesis in A. thaliana and E. grandis. Comparative genomics and bioinformatics analyses of 189 curated gene models of the E. grandis NAC family, one of the largest described to date, revealed extensive tandem duplication in stress response-associated subfamilies, while SCW-associated subfamilies were generally conserved among angiosperms. Novel candidates for wood and tension wood formation as well as cold-stress tolerance were identified from transcriptional profiling in E. globulus and E. grandis. We identified the phenotypic effects and putative targets of the NAC domain TF SND2 in A. thaliana using microarray, microscopy and cell wall chemistry analyses. Moderate SND2 overexpression upregulated genes involved in cellulose, xylan, mannan, signaling and lignin polymerization processes and affected mannose, rhamnose and lignin components of stem cell walls, while strong overexpression resulted in reduced interfascicular fiber SCW deposition. SND2 overexpression in Eucalyptus somatic xylem sectors increased cross-sectional fiber cell area. We optimized a chromatin immunoprecipitation sequencing (ChIP-seq) approach and applied it to developing secondary xylem of mature E. grandis trees to identify the targets of the E. grandis ortholog of SND2, EgrNAC170. In validating the approach, we addressed the regulatory role of the epigenetic mark trimethylated lysine 4 of histone H3 (H3K4me3) in this tissue, showing a strong association with expressed loci, occupation of regions close to transcriptional start sites and tight correlation with transcript abundance, especially that of broadly expressed genes but also genes associated with SCW formation. A pilot study of EgrNAC170 targets was performed using the high-throughput ChIP-seq approach, identifying over 3,000 putative targets in E. grandis developing secondary xylem, but showing evidence that further ChIP-seq data are required for reliable target identification. The results of this thesis contribute to science an understanding of the unique evolution of NAC proteins in Eucalyptus, knowledge of the function of SND2/EgrNAC170 as possible candidates for tree biotechnology, the first genomic profile of a histone modification in developing wood and a high-throughput ChIP-seq protocol for the study of native protein-DNA interactions in developing xylem.
Thesis (PhD)--University of Pretoria, 2014.
Genetics
PhD
Unrestricted

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Anderson, Mary Cloud Bosworth Ammons. "Identification and characterization of a novel transcription factor that regulates NCF2 expression via the TNF-alpha responsive region." Diss., Montana State University, 2007. http://etd.lib.montana.edu/etd/2007/anderson/AndersonM1207.pdf.

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Borrill, Philippa G. M. "The NAM-B1 transcription factor and the control of grain composition in wheat." Thesis, University of East Anglia, 2014. https://ueaeprints.uea.ac.uk/52207/.

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The NAM-B1 transcription factor increases grain protein content, alters grain micronutrient content and accelerates monocarpic senescence, often without imposing a yield penalty. The aim of this thesis was to understand the mechanisms by which NAM-B1 influences nutrient remobilisation and monocarpic senescence to cause these effects. To achieve this I have examined the expression patterns of NAM-B1 and its homologues during development. I have studied the effects of NAM-B1 on nutrient transport, photosynthetic capacity and grain filling using a range of molecular biology and physiological techniques. Finally to understand the network of genes which NAM-B1 regulates I have used chromatin-immunoprecipitation followed by next-generation sequencing (ChIP-seq) to identify downstream targets, and compared these to differentially expressed genes in plants with down-regulated expression of NAM-B1 homologues (NAM RNAi plants). I have found that NAM-B1 expression increases after anthesis in both vegetative and reproductive tissues, including the grain. In stem and leaf tissues I identified that NAM genes are highly expressed in the vascular bundles, which might be important for nutrient transport. However I did not find evidence for NAM genes altering xylem or phloem transport. I found that in NAM RNAi plants, grain development was decoupled from flag leaf senescence. In RNAi plants starch synthesis enzymes were less active during the middle of grain filling than in control plants, potentially resulting in the reallocation of photosynthate to the stems as water soluble carbohydrates. Many of the putative NAM-B1 target genes identified by ChIP-seq have functions related to photosynthesis and validation of these candidate genes is ongoing. In summary I have identified putative NAM-B1 target genes and found that NAM-B1 may act in a tissue specific manner to regulate monocarpic senescence and grain filling. Furthermore I have highlighted novel functions related to carbohydrate metabolism in stems and the grain.

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Частини книг з теми ""NAC transcription factors""

Pascual, Mª Belén, Fernando de la Torre, Rafael A. Cañas, Francisco M. Cánovas, and Concepción Ávila. "NAC Transcription Factors in Woody Plants." In Progress in Botany, 195–222. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/124_2018_19.

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Hoang, Xuan Lan Thi, Yen-Nhi Hoang Nguyen, Nguyen Phuong Thao, and Lam-Son Phan Tran. "NAC Transcription Factors in Drought and Salinity Tolerance." In Salt and Drought Stress Tolerance in Plants, 351–66. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-40277-8_14.

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Jan, Sami Ullah, Muhammad Jamil, Muhammad Faraz Bhatti, and Alvina Gul. "Hallmark Attributes of Plant Transcription Factors and Potentials of WRKY, MYB and NAC in Abiotic Stresses." In Approaches for Enhancing Abiotic Stress Tolerance in Plants, 441–58. Boca Raton, FL : CRC Press, Taylor & Francis Group, 2019.: CRC Press, 2019. http://dx.doi.org/10.1201/9781351104722-25.

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Sharma, Manoj K., Ashu Singh, and Rakesh Singh Sengar. "Bioengineering of DREB and NAC Transcriptional Factors for Enhanced Plant Tolerance Against Abiotic Stresses." In Eco-friendly Agro-biological Techniques for Enhancing Crop Productivity, 173–211. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-6934-5_9.

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Welner, Ditte H., Farah Deeba, Leila Lo Leggio, and Karen Skriver. "NAC Transcription Factors: From Structure to Function in Stress-Associated Networks." In Plant Transcription Factors, 199–212. Elsevier, 2016. http://dx.doi.org/10.1016/b978-0-12-800854-6.00013-0.

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Ramadoss, Bharathi Raja, Manu Pratap Gangola, and Selvakumar Gurunathan. "NAC transcription factor family in rice: Recent advancements in the development of stress-tolerant rice." In Transcription Factors for Abiotic Stress Tolerance in Plants, 47–61. Elsevier, 2020. http://dx.doi.org/10.1016/b978-0-12-819334-1.00004-6.

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Johnson, Derek, and Manisha Patel. "Metabolic and Redox Alterations by Ketogenic Diets." In Ketogenic Diet and Metabolic Therapies, edited by Susan A. Masino, Detlev Boison, Dominic P. D’Agostino, Eric H. Kossoff, and Jong M. Rho, 364–70. Oxford University Press, 2022. http://dx.doi.org/10.1093/med/9780197501207.003.0030.

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When there is a shift from glucose utilization (glycolysis) resulting from carbohydrate-restrictive diets like the ketogenic diet, metabolic changes occur, and acetyl-CoA is instead derived from the alternative parallel processes of gluconeogenesis and fatty acid oxidation. Under these conditions, several antioxidant pathways are amplified, including the transcription factor Nrf2, the Forkhead box pathway, the NAD⁺:NADH ratio, and uncoupling proteins. Additionally, amino acid metabolism and synthesis are modified, with metabolomic analysis isolating tryptophan metabolism as a primary altered pathway. As the field of metabolism is revisited by epilepsy researchers, and animal models are guided by precision medicine, the connections between redox processes and metabolism will be further illuminated.

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Powell, Catherine A., Jian Zhang, John D. Bowman, and Mahua Choudhury. "Resveratrol." In Emerging Applications, Perspectives, and Discoveries in Cardiovascular Research, 288–308. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-2092-4.ch016.

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Cardiovascular disease (CVD) is the leading cause of death in both men and women and has largely been attributed to genetic makeup and lifestyle factors. However, genetic regulation does not fully explain the pathophysiology. Recently, epigenetic regulation, the regulation of the genetic code by modifications that affect the transcription and translation of target genes, has been shown to be important. Silent information regulator-2 proteins or sirtuins are an epigenetic regulator family of class III histone deacetylases (HDACs), unique in their dependency on coenzyme NAD+, that are postulated to mediate the beneficial effects of calorie restriction, thus promoting longevity by reducing the incidence of chronic diseases such as cancer, diabetes, and CVD. Emerging evidence shows that SIRT1 is ubiquitously expressed throughout the body. Resveratrol, a plant polyphenol, has cardioprotective effects and its mechanism of action is attributed to regulation of SIRT1. Incoproation of resveratrol into the diet may be a powerful therapeutic option for the prevention and treatment of CVD.

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Тези доповідей конференцій з теми ""NAC transcription factors""

El-Esawi, Mohamed A. "Functional Role of NAC Transcription Factors in Stress Responses and Genetic Diversity of Rice Plants Grown under Salt Stress Conditions." In 1st International Electronic Conference on Biological Diversity, Ecology and Evolution. Basel, Switzerland: MDPI, 2021. http://dx.doi.org/10.3390/bdee2021-09532.

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Yanwei Wang, Jinbao Pan, Jun Han, Qiuzhi Zhang, Qingpeng Sun, and Yulan Hao. "Cloning of NAC transcription factor fragment in maize." In 2011 International Conference on Remote Sensing, Environment and Transportation Engineering (RSETE). IEEE, 2011. http://dx.doi.org/10.1109/rsete.2011.5965894.

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Roberts, Michael, Nicole Briceno, Jamie Bugel, Catherine Campbell, Mary Dickinson, Trevor McCarthy, Phoebe Oldach, Natalie Stanley, and Jeffrey Forrester. "Abstract 4202: Genetic re-programming of the AML cell line HL-60 during differentiation: Roles of the EGR/NAB and NR4A transcription factors." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-4202.

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Grayck, Eva N., Emily Gibson, Radu Moldovan, Tanya Hartney, and Moshe Levi. "Extracellular Superoxide Changes Intracellular ROS And NAD(P)H Lifetime As Well As Intracellular Signaling Via ERK1/2 To Upregulate A Redox Sensitive Transcription Factor, Egr-1 In Pulmonary Artery Smooth Muscle Cells." In American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado. American Thoracic Society, 2011. http://dx.doi.org/10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a3765.

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Chen, Kok Hao, and Jong Hyun Choi. "Nanoparticle-Aptamer: An Effective Growth Inhibitor for Human Cancer Cells." In ASME 2009 International Mechanical Engineering Congress and Exposition. ASMEDC, 2009. http://dx.doi.org/10.1115/imece2009-11966.

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Semiconductor nanocrystals have unique optical properties due to quantum confinement effects, and a variety of promising approaches have been devised to interface the nanomaterials with biomolecules for bioimaging and therapeutic applications. Such bio-interface can be facilitated via a DNA template for nanoparticles as oligonucleotides can mediate the aqueous-phase nucleation and capping of semiconductor nanocrystals.[1,2] Here, we report a novel scheme of synthesizing fluorescent nanocrystal quantum dots (NQDs) using DNA aptamers and the use of this biotic/abiotic nanoparticle system for growth inhibition of MCF-7 human breast cancer cells for the first time. Particularly, we used two DNA sequences for this purpose, which have been developed as anti-cancer agents: 5-GGT GGT GGT GGT TGT GGT GGT GGT GG-3 (also called, AGRO) and 5-(GT)15-3.[3–5] This study may ultimately form the basis of unique nanoparticle-based therapeutics with the additional ability to optically report molecular recognition. Figure 1a shows the photoluminescence (PL) spectra of GT- and AGRO-passivated PbS QD that fluoresce in the near IR, centered at approximately 980 nm. A typical synthesis procedure involves rapid addition of sodium sulfide in the mixture solution of DNA and Pb acetate at a molar ratio of 2:4:1. The resulting nanocrystals are washed to remove unreacted DNA and ions by adding mixture solution of NaCl and isopropanol, followed by centrifugation. The precipitated nanocrystals are collected and re-suspended in aqueous solution by mild sonication. Optical absorption measurements reveal that approximately 90 and 77% of GT and AGRO DNA is removed after the washing process. The particle size distribution in Figure 1b suggests that the GT sequence-capped PbS particles are primarily in 3–5 nm diameter range. These nanocrystals can be easily incorporated with mammalian cells and remain highly fluorescent in sub-cellular environments. Figure 1c serially presents an optical image of a MCF-7 cell and a PL image of the AGRO-capped QD incorporated with the cell. Figure 1. (a) Normalized fluorescence spectra of PbS QD synthesized with GT and AGRO sequences, which were previously developed as anti-cancer agents. The DNA-capped QD fluoresce in the near IR centered at ∼980 nm. (b) TEM image of GT-templated nanocrystals ranging 3–5 nm in diameter. (c) Optical image of an MCF-7 human breast cancer cell after a 12-hour exposure to aptamer-capped QD. (d) PL image of AGRO-QD incorporated with the cell, indicating that these nanocrystals remain highly fluorescent in sub-cellular environments. One immediate concern for interfacing inorganic nanocrystals with cells and tissue for labeling or therapeutics is their cytotoxicity. The nanoparticle cytotoxicity is primarily determined by material composition and surface chemistry, and QD are potentially toxic by generating reactive oxygen species or by leaching heavy metal ions when decomposed.[6] We examined the toxicity of aptamer-passivated nanocrystals with NIH-3T3 mouse fibroblast cells. The cells were exposed to PbS nanocrystals for 2 days before a standard MTT assay as shown in Figure 2, where there is no apparent cytotoxicity at these doses. In contrast, Pb acetate exerts statistically significant toxicity. This observation suggests a stable surface passivation by the DNA aptamers and the absence of appreciable Pb2+ leaching. Figure 2. Viability of 3T3 mouse fibroblast cells after a 2-day exposure to DNA aptamer-capped nanocrystals. There is no apparent dose-dependent toxicity, whereas a statistically significant reduction in cell viability is observed with Pb ions. Note that Pb acetate at 133 μM is equivalent to the Pb2+ amount that was used for PbS nanocrystal synthesis at maximum concentration. Error bars are standard deviations of independent experiments. *Statistically different from control (p<0.005). Finally, we examined if these cyto-compatible nanoparticle-aptamers remained therapeutically active for cancer cell growth inhibition. The MTT assay results in Figure 3a show significantly decreased growth of breast cancer cells incorporated with AGRO, GT, and the corresponding templated nanocrystals, as anticipated. In contrast, 5-(GC)15-3 and the QDs synthesized with the same sequence, which were used as negative controls along with zero-dose control cells, did not alter cell viability significantly. Here, we define the growth inhibition efficacy as (100 − cell viability) per DNA of a sample, because the DNA concentration is significantly decreased during the particle washing. The nanoparticle-aptamers demonstrate 3–4 times greater therapeutic activities compared to the corresponding aptamer drugs (Figure 3b). We speculate that when a nanoparticle-aptamer is internalized by the cancer cells, it forms an intracellular complex with nucleolin and nuclear factor-κB (NF-κB) essential modulator, thereby inhibiting NF-κB activation that would cause transcription of proliferation and anti-apoptotic genes.[7] The nanoparticle-aptamers may more effectively block the pathways for creating anti-apoptotic genes or facilitate the cellular delivery of aptamers via nanoparticle uptake. Our additional investigation indicates that the same DNA capping chemistry can be utilized to produce aptamer-mediated Fe3O4 nanocrystals, which may be potentially useful in MRI and therapeutics, considering their magnetic properties and biocompatibility. In summary, the nanoparticle-based therapeutic schemes developed here should be valuable in developing a multifunctional drug delivery and imaging agent for biological systems. Figure 3. Anti-proliferation of MCF-7 human breast cancer cells with aptamer-passivated nanocrystals. (a) Viability of MCF-7 cells exposed to AGRO and GT sequences, and AGRO-/GT-capped QD for 7 days. The DNA concentration was 10 uM, while the particles were incubated with cells at 75 nM. (b) Growth inhibition efficacy is defined as (100 − cell viability) per DNA to correct the DNA concentration after particle washing.

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Звіти організацій з теми ""NAC transcription factors""

Dubcovsky, Jorge, Tzion Fahima, Ann Blechl, and Phillip San Miguel. Validation of a candidate gene for increased grain protein content in wheat. United States Department of Agriculture, January 2007. http://dx.doi.org/10.32747/2007.7695857.bard.

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High Grain Protein Content (GPC) of wheat is important for improved nutritional value and industrial quality. However, selection for this trait is limited by our poor understanding of the genes involved in the accumulation of protein in the grain. A gene with a large effect on GPC was detected on the short arm of chromosome 6B in a Triticum turgidum ssp. dicoccoides accession from Israel (DIC, hereafter). During the previous BARD project we constructed a half-million clones Bacterial Artificial Chromosome (BAC) library of tetraploid wheat including the high GPC allele from DIC and mapped the GPC-B1 locus within a 0.3-cM interval. Our long-term goal is to provide a better understanding of the genes controlling grain protein content in wheat. The specific objectives of the current project were to: (1) complete the positional cloning of the GPC-B1 candidate gene; (2) characterize the allelic variation and (3) expression profile of the candidate gene; and (4) validate this gene by using a transgenic RNAi approach to reduce the GPC transcript levels. To achieve these goals we constructed a 245-kb physical map of the GPC-B1 region. Tetraploid and hexaploid wheat lines carrying this 245-kb DIC segment showed delayed senescence and increased GPC and grain micronutrients. The complete sequencing of this region revealed five genes. A high-resolution genetic map, based on approximately 9,000 gametes and new molecular markers enabled us to delimit the GPC-B1 locus to a 7.4-kb region. Complete linkage of the 7.4-kb region with earlier senescence and increase in GPC, Zn, and Fe concentrations in the grain suggested that GPC-B1 is a single gene with multiple pleiotropic effects. The annotation of this 7.4-kb region identified a single gene, encoding a NAC transcription factor, designated as NAM-B1. Allelic variation studies demonstrated that the ancestral wild wheat allele encodes a functional NAC transcription factor whereas modern wheat varieties carry a non-functional NAM-B1 allele. Quantitative PCR showed that transcript levels for the multiple NAMhomologues were low in flag leaves prior to anthesis, after which their levels increased significantly towards grain maturity. Reduction in RNA levels of the multiple NAMhomologues by RNA interference delayed senescence by over three weeks and reduced wheat grain protein, Zn, and Fe content by over 30%. In the transgenic RNAi plants, residual N, Zn and Fe in the dry leaves was significantly higher than in the control plants, confirming a more efficient nutrient remobilization in the presence of higher levels of GPC. The multiple pleiotropic effects of NAM genes suggest a central role for these genes as transcriptional regulators of multiple processes during leaf senescence, including nutrient remobilization to the developing grain. The cloning of GPC-B1 provides a direct link between the regulation of senescence and nutrient remobilization and an entry point to characterize the genes regulating these two processes. This may contribute to their more efficient manipulation in crops and translate into food with enhanced nutritional value. The characterization of the GPC-B1 gene will have a significant impact on wheat production in many regions of the world and will open the door for the identification of additional genes involved in the accumulation of protein in the grain.

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Ori, Naomi, and Mark Estelle. Role of GOBLET and Auxin in Controlling Organ Development and Patterning. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7697122.bard.

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The size and shape of plant leaves are extremely diverse within and among species, and are also sensitive to growth conditions. Compound leaves, such as those of tomato, maintain morphogenetic activity during early stages of their development, enabling them to elaborate lateral appendages such as leaflets. The aim of the research project was to understand the interaction between the plant hormone auxin, the putative auxin response inhibitor ENTIRE (E, SlIAA9) and the NAM/CUC transcription factor GOBLET (GOB) in compound-leaf development in tomato (Solanum lycopersicum). The specific aims of the project were: 1. Investigation of the role of GOB in compound-leaf development. 2. Characterization of E function in auxin signaling. 3. Characterization of the role of auxin in compound-leaf development. 4. Investigation of the genetic and molecular interaction between E and GOB. 5. Investigate the role of these factors in fruit development. There were no major changes in these objectives. GOB was shown to mark and promote the boundaries between the leaf and initiating leaflets. Its accurate distribution was found to be required for proper leaflet initiation and separation. E was found to interact with the TIR1 and AFB6 proteins in an auxin-dependant manner, indicating that these are functional auxin receptors that mediate E degradation in the presence of auxin. This was further supported by the stabilization of E by a mutation in domain II of the protein, which is thought to mediate its auxin-dependant degradation. Over expression of this stabilized form in tomato leaves and characterization of the e mutant phenotype and the E expression domain indicated that E acts between initiating leaflets to inhibit auxin response and lamina growth. Generation and analysis of tomato plants expressing the auxin response reporter DR5::VENUS, and analysis of the effect of auxin microapplication or overexpression of an auxin biosynthesis gene, indicated that auxin marks the sites of leaflet initiation and promotes lamina growth. Investigation of the molecular and genetic interaction between auxin, GOB and E revealed a complex network of mutual regulation that is utilized to precisely pattern the leaf margin in a manner that enables the combination of tight control and flexibility. E, auxin and GOB were shown to affect fruit development and fruit set, and in an extension of the project are currently utilized to identify new players that affect these processes. The research project yielded enhanced understanding of the mechanisms of compound leaf patterning and provided tools that will enable the manipulation of leaf shape and fruit set.

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Fridman, Eyal, Jianming Yu, and Rivka Elbaum. Combining diversity within Sorghum bicolor for genomic and fine mapping of intra-allelic interactions underlying heterosis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597925.bard.

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Heterosis, the enigmatic phenomenon in which whole genome heterozygous hybrids demonstrate superior fitness compared to their homozygous parents, is the main cornerstone of modern crop plant breeding. One explanation for this non-additive inheritance of hybrids is interaction of alleles within the same locus. This proposal aims at screening, identifying and investigating heterosis trait loci (HTL) for different yield traits by implementing a novel integrated mapping approach in Sorghum bicolor as a model for other crop plants. Originally, the general goal of this research was to perform a genetic dissection of heterosis in a diallel built from a set of Sorghum bicolor inbred lines. This was conducted by implementing a novel computational algorithm which aims at associating between specific heterozygosity found among hybrids with heterotic variation for different agronomic traits. The initial goals of the research are: (i) Perform genotype by sequencing (GBS) of the founder lines (ii) To evaluate the heterotic variation found in the diallel by performing field trails and measurements in the field (iii) To perform QTL analysis for identifying heterotic trait loci (HTL) (iv) to validate candidate HTL by testing the quantitative mode of inheritance in F2 populations, and (v) To identify candidate HTL in NAM founder lines and fine map these loci by test-cross selected RIL derived from these founders. The genetic mapping was initially achieved with app. 100 SSR markers, and later the founder lines were genotyped by sequencing. In addition to the original proposed research we have added two additional populations that were utilized to further develop the HTL mapping approach; (1) A diallel of budding yeast (Saccharomyces cerevisiae) that was tested for heterosis of doubling time, and (2) a recombinant inbred line population of Sorghum bicolor that allowed testing in the field and in more depth the contribution of heterosis to plant height, as well as to achieve novel simulation for predicting dominant and additive effects in tightly linked loci on pseudooverdominance. There are several conclusions relevant to crop plants in general and to sorghum breeding and biology in particular: (i) heterosis for reproductive (1), vegetative (2) and metabolic phenotypes is predominantly achieved via dominance complementation. (ii) most loci that seems to be inherited as overdominant are in fact achieving superior phenotype of the heterozygous due to linkage in repulsion, namely by pseudooverdominant mechanism. Our computer simulations show that such repulsion linkage could influence QTL detection and estimation of effect in segregating populations. (iii) A new height QTL (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 in sorghum, and its genetic dissection in RIL population demonstrated that it affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. (iv) HTL mapping for grain nitrogen content in sorghum grains has identified several candidate genes that regulate this trait, including several putative nitrate transporters and a transcription factor belonging to the no-apical meristem (NAC)-like large gene family. This activity was combined with another BARD-funded project in which several de-novo mutants in this gene were identified for functional analysis.

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