Relevant bibliographies by topics / Promoters (Genetics)

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Promoters (Genetics)'

Author: Grafiati
Published: 4 June 2021
Last updated: 6 September 2023

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Journal articles on the topic "Promoters (Genetics)"

1

Greener, A., S. M. Lehman, and D. R. Helinski. "Promoters of the broad host range plasmid RK2: analysis of transcription (initiation) in five species of gram-negative bacteria." Genetics 130, no. 1 (January 1, 1992): 27–36. http://dx.doi.org/10.1093/genetics/130.1.27.

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Abstract A broad host range cloning vector was constructed, suitable for monitoring promoter activity in diverse Gram-negative bacteria. This vector, derived from plasmid RSF1010, utilized the firefly luciferase gene as the reporter, since the assay for its bioluminescent product is sensitive, and measurements can be made without background from the host. Twelve DNA fragments with promoter activity were obtained from broad host range plasmid RK2 and inserted into the RSF1010 derived vector. The relative luciferase activities were determined for these fragments in five species of Gram-negative bacteria. In addition, four promoters were analyzed by primer extension to locate transcriptional start sites in each host. The results show that several of the promoters vary substantially in relative strengths or utilize different transcriptional start sites in different bacteria. Other promoters exhibited similar activities and identical start sites in the five hosts examined.
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Li, Jinyang, Sheng Tong, Farrukh Raza Amin, Habiba Khalid, Kai Chen, Xiaoguang Zhao, Jinling Cai, and Demao Li. "Enhancing the Activity of a Self-Inducible Promoter in Escherichia coli through Saturation Mutation and High-Throughput Screening." Fermentation 9, no. 5 (May 13, 2023): 468. http://dx.doi.org/10.3390/fermentation9050468.

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The use of self-inducible promoters is a promising strategy to address metabolic imbalances caused by overexpression. However, the low activity of natural self-inducible promoters hinders their widespread application. To overcome this limitation, we selected the fic promoter as a model promoter to create an enhanced self-inducible promoter library using saturation mutations and high-throughput screening. Sequence analysis revealed that these promoters share certain characteristics, including semi-conservation in the −35 hexamer, highly conserved cytosine in the −17 motif (compared to −13 for other promoters), and moderate A+T content between positions −33 and −18 in the spacer region. Additionally, the discriminator region of these promotors features high A+T content in the first five bases. We identified PficI-17, PficII-33, and PficIII-14 promoters as the optional promoters in the −35 hexamer, spacer region, and discriminator mutation libraries, respectively. These promotors were used as representatives to measure the specific fluorescence and OD600 nm dynamics in different media and to confirm their effect on the expression of different proteins, including egfp (enhanced green fluorescence protein) and rfp (red fluorescence protein). Overall, our findings provide valuable guidance for modifying promoters and developing a promoter library suitable for regulating target genes.
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Mahoney, Michael E., and Daniel L. Wulff. "Mutations that Improve the pRE Promoter of Coliphage Lambda." Genetics 115, no. 4 (April 1, 1987): 591–95. http://dx.doi.org/10.1093/genetics/115.4.591.

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ABSTRACT The dya5 mutation, a C→T change at position -43 of the λ pRE promoter, results in a twofold increase in pRE activity in vivo. Smaller increases in pRE activity are found for the dya2 mutation, a T→C change at position -1 of pRE, and the dya3 mutation, an A→G change at +5 of pRE· The mutant pRE promoters retain complete dependence on cII protein for activity. These observations argue, at least for pRE-like promoters, that promoter activities are influenced by nucleotide sequences at least eight nucleotides to the 5′-side of the conventional -35 region consensus sequence, and by nucleotide sequences near the start-site of transcription. Although Hawley and McClure (1983) found A·T pairs more frequently than G·TC pairs in the region of -40 to -45 of prokaryotic promoters, other mutations that change a G·TC pair to an A·T pair at positions -41, -44 and -45 of pRE do not result in increased promoter activity. We also found that a T→C change at position -42 results in a mild decrease in promoter activity. These observations argue that Ts at positions -42 and -43 of pRE are required for maximum promoter activity, but do not support the hypothesis that As and Ts in the -40 to -45 region generally lead to higher promoter activities.
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Shujaat, Muhammad, Abdul Wahab, Hilal Tayara, and Kil To Chong. "pcPromoter-CNN: A CNN-Based Prediction and Classification of Promoters." Genes 11, no. 12 (December 21, 2020): 1529. http://dx.doi.org/10.3390/genes11121529.

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A promoter is a small region within the DNA structure that has an important role in initiating transcription of a specific gene in the genome. Different types of promoters are recognized by their different functions. Due to the importance of promoter functions, computational tools for the prediction and classification of a promoter are highly desired. Promoters resemble each other; therefore, their precise classification is an important challenge. In this study, we propose a convolutional neural network (CNN)-based tool, the pcPromoter-CNN, for application in the prediction of promotors and their classification into subclasses σ70, σ54, σ38, σ32, σ28 and σ24. This CNN-based tool uses a one-hot encoding scheme for promoter classification. The tools architecture was trained and tested on a benchmark dataset. To evaluate its classification performance, we used four evaluation metrics. The model exhibited notable improvement over that of existing state-of-the-art tools.
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Fandl, J. P., L. K. Thorner, and S. W. Artz. "Mutations that affect transcription and cyclic AMP-CRP regulation of the adenylate cyclase gene (cya) of Salmonella typhimurium." Genetics 125, no. 4 (August 1, 1990): 719–27. http://dx.doi.org/10.1093/genetics/125.4.719.

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Abstract We studied the expression of the cya promoter(s) in cya-lac fusion strains of Salmonella typhimurium and demonstrated cAMP receptor protein (CRP)-dependent repression by cAMP. Expression of cya was reduced about fourfold in cultures grown in acetate minimal medium as compared to cultures grown in glucose-6-phosphate minimal medium. Expression of cya was also reduced about fourfold by addition of 5 mM cAMP to cultures grown in glucose minimal medium. We constructed in vitro deletion and insertion mutations altering a major cya promoter (P2) and a putative CRP binding site overlapping P2. These mutations were recombined into the chromosome by allele replacement with M13mp::cya recombinant phages and the regulation of the mutant promoters was analyzed. A 4-bp deletion of the CRP binding site and a 4-bp insertion in this site nearly eliminated repression by cAMP. A mutant with the P2 promoter and the CRP binding site both deleted exhibited an 80% reduction in cya expression; the 20% residual expression was insensitive to cAMP repression. This mutant retained a Cya+ phenotype. Taken together, the results establish that the cya gene is transcribed from multiple promoters one of which, P2, is negatively regulated by the cAMP-CRP complex. Correction for the contribution to transcription by the cAMP-CRP nonregulated cya promoters indicates that the P2 promoter is repressed at least eightfold by cAMP-CRP.
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Efremova, Larisa N., Svetlana R. Strelnikova, Guzel R. Gazizova, Elena A. Minkina, and Roman A. Komakhin. "A Synthetic Strong and Constitutive Promoter Derived from the Stellaria media pro-SmAMP1 and pro-SmAMP2 Promoters for Effective Transgene Expression in Plants." Genes 11, no. 12 (November 26, 2020): 1407. http://dx.doi.org/10.3390/genes11121407.

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Synthetic promoters are vital for genetic engineering-based strategies for crop improvement, but effective methodologies for their creation and systematic testing are lacking. We report here on the comparative analysis of the promoters pro-SmAMP1 and pro-SmAMP2 from Stellaria media ANTIMICROBIAL PEPTIDE1 (AMP1) and ANTIMICROBIAL PEPTIDE2 (AMP2). These promoters are more effective than the well-known Cauliflower mosaic virus 35S promoter. Although these promoters share about 94% identity, the pro-SmAMP1 promoter demonstrated stronger transient expression of a reporter gene in Agrobacterium infiltration of Nicotiana benthamiana leaves, while the pro-SmAMP2 promoter was more effective for the selection of transgenic tobacco (Nicotiana tabacum) cells when driving a selectable marker. Using the cap analysis of gene expression method, we detected no differences in the structure of the transcription start sites for either promoter in transgenic plants. For both promoters, we used fine-scale deletion analysis to identify 160 bp-long sequences that retain the unique properties of each promoter. With the use of chimeric promoters and directed mutagenesis, we demonstrated that the superiority of the pro-SmAMP1 promoter for Agrobacterium-mediated infiltration is caused by the proline-inducible ACTCAT cis-element strictly positioned relative to the TATA box in the core promoter. Surprisingly, the ACTCAT cis-element not only activated but also suppressed the efficiency of the pro-SmAMP1 promoter under proline stress. The absence of the ACTCAT cis-element and CAANNNNATC motif (negative regulator) in the pro-SmAMP2 promoter provided a more constitutive gene expression profile and better selection of transgenic cells on selective medium. We created a new synthetic promoter that enjoys high effectiveness both in transient expression and in selection of transgenic cells. Intact promoters with differing properties and high degrees of sequence identity may thus be used as a basis for the creation of new synthetic promoters for precise and coordinated gene expression.
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Davey, James A., and Corey J. Wilson. "Engineered signal-coupled inducible promoters: measuring the apparent RNA-polymerase resource budget." Nucleic Acids Research 48, no. 17 (September 5, 2020): 9995–10012. http://dx.doi.org/10.1093/nar/gkaa734.

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Abstract Inducible promoters are a central regulatory component in synthetic biology, metabolic engineering, and protein production for laboratory and commercial uses. Many of these applications utilize two or more exogenous promoters, imposing a currently unquantifiable metabolic burden on the living system. Here, we engineered a collection of inducible promoters (regulated by LacI-based transcription factors) that maximize the free-state of endogenous RNA polymerase (RNAP). We leveraged this collection of inducible promotors to construct simple two-channel logical controls that enabled us to measure metabolic burden – as it relates to RNAP resource partitioning. The two-channel genetic circuits utilized sets of signal-coupled transcription factors that regulate cognate inducible promoters in a coordinated logical fashion. With this fundamental genetic architecture, we evaluated the performance of each inducible promoter as discrete operations, and as coupled systems to evaluate and quantify the effects of resource partitioning. Obtaining the ability to systematically and accurately measure the apparent RNA-polymerase resource budget will enable researchers to design more robust genetic circuits, with significantly higher fidelity. Moreover, this study presents a workflow that can be used to better understand how living systems adapt RNAP resources, via the complementary pairing of constitutive and regulated promoters that vary in strength.
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Hong, Clarice K. Y., and Barak A. Cohen. "Genomic environments scale the activities of diverse core promoters." Genome Research 32, no. 1 (December 27, 2021): 85–96. http://dx.doi.org/10.1101/gr.276025.121.

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A classical model of gene regulation is that enhancers provide specificity whereas core promoters provide a modular site for the assembly of the basal transcriptional machinery. However, examples of core promoter specificity have led to an alternate hypothesis in which specificity is achieved by core promoters with different sequence motifs that respond differently to genomic environments containing different enhancers and chromatin landscapes. To distinguish between these models, we measured the activities of hundreds of diverse core promoters in four different genomic locations and, in a complementary experiment, six different core promoters at thousands of locations across the genome. Although genomic locations had large effects on expression, the intrinsic activities of different classes of promoters were preserved across genomic locations, suggesting that core promoters are modular regulatory elements whose activities are independently scaled up or down by different genomic locations. This scaling of promoter activities is nonlinear and depends on the genomic location and the strength of the core promoter. Our results support the classical model of regulation in which diverse core promoter motifs set the intrinsic strengths of core promoters, which are then amplified or dampened by the activities of their genomic environments.
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George, Janet A., and Mary-Lou Pardue. "The Promoter of the Heterochromatic Drosophila Telomeric Retrotransposon, HeT-A, Is Active When Moved Into Euchromatic Locations." Genetics 163, no. 2 (February 1, 2003): 625–35. http://dx.doi.org/10.1093/genetics/163.2.625.

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Abstract The Drosophila telomeric retrotransposon, HeT-A, is found only in heterochromatin; therefore, its promoter must function in this chromatin environment. Studies of position effect variegation suggest that promoters of heterochromatic genes are very different from euchromatic promoters, but this idea has not been tested with isolated promoter sequences. The HeT-A promoter is the first heterochromatin promoter to be isolated and it is of interest to investigate its activity when removed from telomeric heterochromatin. This promoter was initially characterized by testing reporter constructs in transient transfection of cultured cells, an environment that may approximate its endogenous heterochromatin. We now report P-element-mediated transpositions of these constructs, testing the function of different parts of the putative promoter in euchromatin. Expression of endogenous HeT-A RNA shows marked developmental regulation and accumulates preferentially in replicating diploid tissues. HeT-A promoter constructs are active in all euchromatic locations tested and some display aspects of endogenous HeT-A stage- and cell-type expression programs. The activity of each promoter construct in euchromatic locations is also generally consistent with its activity in the transient transfection tests; a possibly significant exception is one sequence segment that appreciably enhanced activity in transient transfection but repressed promoter activity in euchromatin.
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Wang, Ye, Haochen Wang, Lei Wei, Shuailin Li, Liyang Liu, and Xiaowo Wang. "Synthetic promoter design in Escherichia coli based on a deep generative network." Nucleic Acids Research 48, no. 12 (May 19, 2020): 6403–12. http://dx.doi.org/10.1093/nar/gkaa325.

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Abstract Promoter design remains one of the most important considerations in metabolic engineering and synthetic biology applications. Theoretically, there are 450 possible sequences for a 50-nt promoter, of which naturally occurring promoters make up only a small subset. To explore the vast number of potential sequences, we report a novel AI-based framework for de novo promoter design in Escherichia coli. The model, which was guided by sequence features learned from natural promoters, could capture interactions between nucleotides at different positions and design novel synthetic promoters in silico. We combined a deep generative model that guides the search for artificial sequences with a predictive model to preselect the most promising promoters. The AI-designed promoters were optimized based on the promoter activity in E. coli and the predictive model. After two rounds of optimization, up to 70.8% of the AI-designed promoters were experimentally demonstrated to be functional, and few of them shared significant sequence similarity with the E. coli genome. Our work provided an end-to-end approach to the de novo design of novel promoter elements, indicating the potential to apply deep learning methods to de novo genetic element design.
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Dissertations / Theses on the topic "Promoters (Genetics)"

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Sigvardsson, Mikael. "Regulation of immunoglobulin transcription during B-cell differentiation." Lund : Lund University, 1995. http://books.google.com/books?id=TJNqAAAAMAAJ.

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Bennett, Selester. "The construction and testing of maize transcriptional fusions in yeast (Saccharomyces cerevisiae)." Thesis, This resource online, 1993. http://scholar.lib.vt.edu/theses/available/etd-10312009-020253/.

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Edelman, Lucas Brandon. "Transcriptional correlates of promoter interactions in murine cell nuclei." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648695.

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Ezpeleta, Jessica. "The characterization of the ABF-1 promoter." Scholarly Commons, 2001. https://scholarlycommons.pacific.edu/uop_etds/559.

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The basic helix-loop-helix (bHLH) family oftranscription factors consists of proteins involved in cellular proliferation and differentiation. The HLH structure plays a key role in protein-protein dimerization and with the DNA target sites, referred to as E boxes containing the consensus DNA sequence CANNTG. One class of mammalian class I bHLH proteins includes products of the E2A gene, which result from alternative splicing (E12, E47, and ITF), E2-2 and HEB. E2A proteins have also been detected in most cell lines with high levels of expression in lymphoid- and pancreatic cells. It has also been demonstrated that E2A is required for B cell maturation, T cell development and has been shown to function as tumor suppressors. To date, an E2A-interacting bHLH transcription factor largely restricted to activated B lymphocytes, called ABF -1, was isolated using the two-hybrid system. ABF -1 is the only B cell restricted bHLH protein isolated. ABF-1/E2A heterodimers have been detected in B lymphocytes. In these studies, the mapping of the ABF-1 promoter and the critical 5' regulatory elements that control ABF-1 gene expression were analyzed through 5' deletional analysis. 5' -DNA flanking pieces of the promoter region were created through PCR and inserted into a promoterless cloning vector containing the firefly luciferase reporter gene. RT -PCR analysis and anchored PCR was utilized to demonstrate the transcriptional activity of the - promoter region of the ABF-1 gene. Transient transfections were completed to determine critical regulatory sequences. The promoter location was confirmed through computer analysis of the nucleotide sequence and deletional analysis.
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Chan, Tung-lei, and 陳冬妮. "Promoter characterization of testis specific protein, Y-linked like2 (TSPYL2)." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B41290410.

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Chan, Tung-lei. "Promoter characterization of testis specific protein, Y-linked like 2 (TSPYL2)." Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/B41290410.

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Schoep, Tobias Delavilla. "Isolation and characterization of Pseudobutyrivibrio ruminis gene promoters." Schoep, Tobias Delavilla (2004) Isolation and characterization of Pseudobutyrivibrio ruminis gene promoters. PhD thesis, Murdoch University, 2004. http://researchrepository.murdoch.edu.au/294/.

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A family of E. coli - P. ruminis shuttle-plasmids was constructed to allow the isolation and characterization of gene promoters from the rumen bacterium P. ruminis. The promoter rescue plasmid pBK was used to isolate a total of 4 genomic DNA fragments that promoted transcription in P. ruminis strains 0/10. These promoters, and an additional promoter, previously isolated from P. ruminis strain OR38 (Schoep, 1999), were identified by their ability to initiate expression of a promoterless ermAM gene in P. ruminis. Within 4 of the fragments, a total of 5 transcription start sites were identified in P. ruminis using a novel, fluorescent-primer extension analysis protocol. Comparison of promoters isolated in this and previous studies revealed a strong consensus RNA polymerase DNA-binding motif, including the well characterized -35 and -10 elements. Consensus sequences established for these elements were: TTgacA and AtAATAta respectively, where bold upper-case font, regular upper-case, and lower-case fonts represent conservation in 100%, 80%, and 70% of promoters respectively. The -10 and -35 motifs were interspaced by 16 - 18 nt. Among the newly identified promoters, the consensus for the -10 element was extended one nucleotide upstream and downstream of the standard hexamer (boxed). These motifs were similar to those recognized by eubacterial RNA polymerase containing the alpha -70 like factor. Promoters also contained possible UP elements, and were significantly more curved than protein-coding regions. Additional plasmid vectors were constructed, to allow the use of both the quantitative SYBR green real time PCR and beta-glucuronidase assays, to examine 4 promoters in depth. This showed a wide range of promoter strengths within the group. However, no correlation was found between the composition and context of elements within P. ruminis promoters, and promoter strength. A mutation within the -35 element of one promoter revealed that promoter strength, and the choice of transcription start site were both sensitive to single nucleotide
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Zaugg, Judith Barbara. "A computational study of promoter structure and transcriptional regulation in yeast on a genomic scale." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609838.

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Lloyd, Amanda Lian. "Cloning, characterisation and sequencing of promoters of Helicobacter pylori 4187E /." Connect to this title, 2004. http://theses.library.uwa.edu.au/adt-WU2005.0112.

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Govender, Cindy. "Stem specific promoters from sorghum and maize for use in sugarcane." Thesis, Stellenbosch : Stellenbosch University, 2008. http://hdl.handle.net/10019.1/2374.

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Thesis (MSc (Genetics. Institute of Plant Biotechnology))--Stellenbosch University, 2008.
Sugarcane (Saccharum spp.) is an important crop which is cultivated worldwide for the high sucrose content in its stem. Conventional plant breeding has proven to be very successful over the years with regard to the enhancement of yield characteristics but due to the exhaustion of genetic potential in the commercial sugarcane germplasm recent progress has been slow. Genetic engineering seems to be a more attractive approach to enhance sucrose content and pest resistance in the stems but requires appropriate transgenes and suitable promoter. A promoter is essential to drive the transcription of a gene and is therefore critical to the success of transgenic approaches in sugarcane crop improvement. A negligible number of strong stem-specific promoters is available for use in sugarcane and this is one of the major limitations to genetic engineering. The goal of this project was to isolate a stemspecific promoter from maize and sorghum to drive stem-specific transgene expression in sugarcane. The approach used was to source promoters from non-sugarcane grass species with less complex genomes to simplify isolation and possibly counteract silencing. A cDNA sequence (SS) (EST clone, Accession number AW746904) from sugarcane was shown by Northern and Southern analysis to be stem-specific and to have an appropriately low copy number. The SS gene sequence was not expressed in the leaves of maize, sorghum or the sugarcane cultivars and prominent expression was observed only in the stems of the sugarcane hybrids N19 and 88H0019. The SS gene sequence was used to isolate its upstream regions from a Lambda genomic library of maize (Zea mays) and a sorghum (Sorghum bicolor) Bacterial Artificial Chromosome library (BAC). Of the four sorghum and six maize clones obtained in this study, a 4500 bp maize genomic DNA fragment (λ5) was sub-cloned in three fragments into separate pBluescript vectors using the ‘forced’ cloning approach for sequence and database (BLASTN) analysis. This revealed the complete SS gene sequence (975 bp), the promoter and a 300 bp intron region. A stretch of DNA sequence from nucleotides 664-3194 from the maize clone 5 sequence was designated the maize5-pro. Following sequence alignment of the maize and sugarcane promoter regions, significant sequence identity (68%) was observed between nucleotide 1675 and 3194 in maize and nucleotide 1506 and 2947 in sugarcane. The distance between the putative TATA-box and the TSS for this promoter (30 bp) was found to fall within the expected range of 32± 7 bp. The promoter region was analysed for possible cis-acting regulatory elements and revealed several promoter elements that are common in other plant promoters. The comparisons made between the putative transcription factors in maizepro-5 and the sugarcane promoter show that both promoter sequences are very similar as they share ten of the same transcription factors. However, the transcriptional factors WBOX, SRE and SP8BFIBSP8BIB are unique to the maize5-pro and the TAAG motif to the sugarcane promoter. Primers were designed with appropriate restriction sites and the promoter and intron (2850 bp) region was amplified by PCR (Polymerase chain reaction). The amplified fragment was fused inframe to the GUS reporter gene encoding β-glucuronidase to produce a transformation test vector. This will be used in future work to assess the functionality of the promoter through the production of stable transformants in which GUS activity can be measured in a range of tissues.
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Books on the topic "Promoters (Genetics)"

1

Lutz, Nover, ed. Plant promoters and transcription factors. Berlin: Springer-Verlag, 1994.

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Lawrence, Privalsky Martin, ed. Transcriptional corepressors: Mediators of eukaryotic gene repression. Berlin: Springer, 2001.

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EPA Workshop on the Development of Risk Assessment Methodologies for Tumor Promoters (1987 Bethesda, Md.). Report of the EPA Workshop on the development of risk assessment methodologies for tumor promoters. Washington, DC: Office of Health and Environmental Assessment and Office of Regulatory Support and Scientific Analysis, Office of Research and Development, U.S. Environmental Protection Agency, 1987.

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EPA Workshop on the Development of Risk Assessment Methodologies for Tumor Promoters (1987 Bethesda, Md.). Report of the EPA Workshop on the Development of Risk Assessment Methodologies for Tumor Promoters: Project summary. Washington, D.C: U.S. Environmental Protection Agency, Office of Health and Environmental Assessment, 1988.

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Bryan, Cullen, and Roche-UCLA Symposium on Mechanisms of Control of Gene Expression (1987 : Steamboat Springs, Colo.), eds. Mechanisms of control of gene expression: Proceedings of a Roche-UCLA Symposium, held at Steamboat Springs, Colorado, March 29-April 4, 1987. New York: Liss, 1988.

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Ponnambalam, Sreenivasan. Transcription initiation at the 'Escherichia Coli' galactose Operon promoter region: Genetic and biochemicalstudies. Birmingham: University of Birmingham, 1988.

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H, Colburn Nancy, Moses Harold L, and Stanbridge Eric J, eds. Growth factors, tumor promoters and cancer genes: Proceedings of a Triton Biosciences UCLA Symposium held in Steamboat Springs, Colorado, April 6-13, 1986. New York: Liss, 1988.

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Triton Biosciences-UCLA Symposium (1986 Steamboat Springs, Colo.). Growth factors, tumor promoters, and cancer genes: Proceedings of a Triton Biosciences-UCLA Symposium held in Steamboat Springs, Colorado, April 6-13, 1986. Edited by Colburn Nancy H, Moses Harold L, and Stanbridge Eric J. New York: Liss, 1988.

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1939-, Chitsike L. T., ed. Intellectual property rights and genetic resources: Guidelines for developing sui generis national policies and legislation to promote community and farmers' interests for southern Africa. Harare, Zimbabwe: IUCN, Regional Office for Southern Africa, 2001.

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Latchman, David S. Eukaryotic transcription factors. 5th ed. Amsterdam: Elsevier/Academic Press, 2008.

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Book chapters on the topic "Promoters (Genetics)"

1

Lamb, C. J., and R. A. Dixon. "Properties of Plant Defense Gene Promoters." In Advances in Molecular Genetics of Plant-Microbe Interactions Vol. 1, 367–72. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-015-7934-6_57.

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Legocki, Roman P., Misuk Legocki, Thomas O. Baldwin, and Aladar A. Szalay. "Bioluminescence in Root Nodules of Soybean Controlled by Nitrogenase Promoters." In Molecular genetics of plant-microbe interactions, 282–87. Dordrecht: Springer Netherlands, 1987. http://dx.doi.org/10.1007/978-94-009-4482-4_71.

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Henschke, Rolf B., and Friedrich R. J. Schmidt. "Use of wide host range promoters to monitor the fate of recombinant DNA in soil." In Bacterial Genetics in Natural Environments, 200–206. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-009-1834-4_15.

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Spaink, Herman P., Rob J. H. Okker, Carel A. Wijffelman, Elly Pees, and Ben J. J. Lugtenberg. "Regulation of the Promoters in the Nodulation Region of the Symbiosis Plasmid pRL1JI of Rhizobium Leguminosarum." In Molecular genetics of plant-microbe interactions, 244–46. Dordrecht: Springer Netherlands, 1987. http://dx.doi.org/10.1007/978-94-009-4482-4_61.

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Djordjevic, G. M., and T. R. Klaenhammer. "A method for mapping phage-inducible promoters for use in bacteriophage-triggered defense systems." In Methods for studying the genetics, molecular biology, physiology, and pathogenesis of the streptococci, 119–26. Dordrecht: Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-017-2258-2_14.

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Guilfoyle, Tom J. "The Structure of Plant Gene Promoters." In Genetic Engineering, 15–47. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4615-5925-2_2.

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Pelham, Hugh. "Properties and Uses of Heat Shock Promoters." In Genetic Engineering, 27–44. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4684-5377-5_2.

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Komarnytsky, Slavko, and Nikolai Borisjuk. "Functional Analysis of Promoter Elements in Plants." In Genetic Engineering, 113–41. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4615-0073-5_6.

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Reuter, Ingmar, Thomas Werner, and Edgar Wingender. "Computer-Assisted Methods for the Identification and Characterization of Polymerase II Promoters." In Genetic Engineering, 25–40. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4899-1739-3_2.

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Santos, Efrén, Ricardo Pacheco, Liliana Villao, Luis Galarza, Daniel Ochoa, Carlos Jordán, and José Flores. "Promoter Analysis in Banana." In Banana: Genomics and Transgenic Approaches for Genetic Improvement, 157–79. Singapore: Springer Singapore, 2016. http://dx.doi.org/10.1007/978-981-10-1585-4_11.

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Conference papers on the topic "Promoters (Genetics)"

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"Stress-inducible and tissue-specific promoters in transgenic tomatoes." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-180.

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"New antimicrobial gene promoters from chickweed (Stellaria media) for biotechnology of cultivated plants." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-048.

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"New efficient gene promoters from Stellaria media for plant genetic engineering." In Current Challenges in Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences Novosibirsk State University, 2019. http://dx.doi.org/10.18699/icg-plantgen2019-42.

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Ho, Tuan-hua David, Chwan-Yang Hong, Ming-Tsair Chan, and Sumay Yu. "Designing and constructing novel gene promoters to generate stress-tolerant plants without yield penalty." In Proceedings of the Fifth International Rice Genetics Symposium. World Scientific Publishing Company, 2007. http://dx.doi.org/10.1142/9789812708816_0022.

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Frénoy, Antonine, François Taddei, and Dusan Misevic. "Constrained Genetic Architecture Promotes Cooperation." In Artificial Life 14: International Conference on the Synthesis and Simulation of Living Systems. The MIT Press, 2014. http://dx.doi.org/10.7551/978-0-262-32621-6-ch004.

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"Analysis of the activity of the DR5 promoter in tuber-forming plants." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-111.

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"The knockout of predicted MYB60 gene in Eruca sativa promotes anthocyanin accumulation." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-094.

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Smatti, Maria K., Yasser Al-Sarraj, Omar Albagha, and Hadi M. Yassine. "Host Genetic Variants Potentially Associated with SARS-Cov-2: A Multi-Population Analysis." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0298.

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Background: Clinical outcomes of Coronavirus Disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed enormous inter-individual and interpopulation differences, possibly due to host genetics differences. Earlier studies identified single nucleotide polymorphisms (SNPs) associated with SARS-CoV-1 in Eastern Asian (EAS) populations. In this report, we aimed at exploring the frequency of a set of genetic polymorphisms that could affect SARS-CoV-2 susceptibility or severity, including those that were previously associated with SARS-CoV-1. Methods: We extracted the list of SNPs that could potentially modulate SARS-CoV-2 from the genome wide association studies (GWAS) on SARS-CoV-1 and other viruses. We also collected the expression data of these SNPs from the expression quantitative trait loci (eQTLs) databases. Sequences from Qatar Genome Programme (QGP, n=6,054) and 1000Genome project were used to calculate and compare allelic frequencies (AF). Results: A total of 74 SNPs, located in 10 genes: ICAM3, IFN-γ, CCL2, CCL5, AHSG, MBL, Furin, TMPRSS2, IL4, and CD209 promoter, were identified. Analysis of Qatari genomes revealed significantly lower AF of risk variants linked to SARS-CoV-1 severity (CCL2, MBL, CCL5, AHSG, and IL4) compared to that of 1000Genome and/or the EAS population (up to 25-fold change). Conversely, SNPs in TMPRSS2, IFN-γ, ICAM3, and Furin were more common among Qataris (average 2-fold change). Inter-population analysis showed that the distribution of risk alleles among Europeans differs substantially from Africans and EASs. Remarkably, Africans seem to carry extremely lower frequencies of SARS-CoV-1 susceptibility alleles, reaching to 32-fold decrease compared to other populations. Conclusion: Multiple genetic variants, which could potentially modulate SARS-CoV-2 infection, are significantly variable between populations, with the lowest frequency observed among Africans. Our results highlight the importance of exploring population genetics to understand and predict COVID-19 outcomes. Indeed, further studies are needed to validate these findings as well as to identify new genetic determinants linked to SARS-CoV-2.
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Singh, Abhyudai, Cesar A. Vargas, and Rajesh Karmakar. "Stochastic analysis of genetic promoter architectures with memory." In 2013 IEEE 52nd Annual Conference on Decision and Control (CDC). IEEE, 2013. http://dx.doi.org/10.1109/cdc.2013.6761034.

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Byeon, B., and K. Rasheed. "Bayesian Networks and Genetic Algorithms for Promoter Recognition." In IASTED Technology Conferences 2010. Calgary,AB,Canada: ACTAPRESS, 2010. http://dx.doi.org/10.2316/p.2010.728-030.

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Reports on the topic "Promoters (Genetics)"

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Brinckerhoff, Constance E. Genetic Analysis of a Single Nucleotide Polymorphism in the Matrix Metalloproteinase 1 Promoter in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, July 2002. http://dx.doi.org/10.21236/ada407580.

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Brinckerhoff, Constqance B. Genetic Analysis of a Single Nucleotide Polymorphism in the Matrix Metalloproteinase 1 Promoter in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, July 2003. http://dx.doi.org/10.21236/ada419338.

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Norelli, John L., Moshe Flaishman, Herb Aldwinckle, and David Gidoni. Regulated expression of site-specific DNA recombination for precision genetic engineering of apple. United States Department of Agriculture, March 2005. http://dx.doi.org/10.32747/2005.7587214.bard.

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Objectives: The original objectives of this project were to: 1) evaluate inducible promoters for the expression of recombinase in apple (USDA-ARS); 2) develop alternative selectable markers for use in apple to facilitate the positive selection of gene excision by recombinase (Cornell University); 3) compare the activity of three different recombinase systems (Cre/lox, FLP/FRT, and R/RS)in apple using a rapid transient assay (ARO); and 4) evaluate the use of recombinase systems in apple using the best promoters, selectable markers and recombinase systems identified in 1, 2 and 3 above (Collaboratively). Objective 2 was revised from the development alternative selectable markers, to the development of a marker-free selection system for apple. This change in approach was taken due to the inefficiency of the alternative markers initially evaluated in apple, phosphomannose-isomerase and 2-deoxyglucose-6-phosphate phosphatase, and the regulatory advantages of a marker-free system. Objective 3 was revised to focus primarily on the FLP/FRT recombinase system, due to the initial success obtained with this recombinase system. Based upon cooperation between researchers (see Achievements below), research to evaluate the use of the FLP recombinase system under light-inducible expression in apple was then conducted at the ARO (Objective 4). Background: Genomic research and genetic engineering have tremendous potential to enhance crop performance, improve food quality and increase farm profits. However, implementing the knowledge of genomics through genetically engineered fruit crops has many hurdles to be overcome before it can become a reality in the orchard. Among the most important hurdles are consumer concerns regarding the safety of transgenics and the impact this may have on marketing. The goal of this project was to develop plant transformation technologies to mitigate these concerns. Major achievements: Our results indicate activity of the FLP\FRTsite-specific recombination system for the first time in apple, and additionally, we show light- inducible activation of the recombinase in trees. Initial selection of apple transformation events is conducted under dark conditions, and tissue cultures are then moved to light conditions to promote marker excision and plant development. As trees are perennial and - cross-fertilization is not practical, the light-induced FLP-mediated recombination approach shown here provides an alternative to previously reported chemically induced recombinase approaches. In addition, a method was developed to transform apple without the use of herbicide or antibiotic resistance marker genes (marker free). Both light and chemically inducible promoters were developed to allow controlled gene expression in fruit crops. Implications: The research supported by this grant has demonstrated the feasibility of "marker excision" and "marker free" transformation technologies in apple. The use of these safer technologies for the genetic enhancement of apple varieties and rootstocks for various traits will serve to mitigate many of the consumer and environmental concerns facing the commercialization of these improved varieties.
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Strauss, S. H., V. Busov, K. Kosola, J. Kennedy, J. Morrell, C. Ma, A. Elias, and E. Etherington. Genetic modification of gibberellic acid signaling to promote carbon sequestration in tree roots and stems. Office of Scientific and Technical Information (OSTI), May 2009. http://dx.doi.org/10.2172/952484.

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Busov, Victor. GENETIC MODIFICATION OF GIBBERELLIC ACID SIGNALING TO PROMOTE CARBON SEQUESTRATION IN TREE ROOTS AND STEMS. Office of Scientific and Technical Information (OSTI), March 2013. http://dx.doi.org/10.2172/1067341.

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Jung, Carina, Karl Indest, Matthew Carr, Richard Lance, Lyndsay Carrigee, and Kayla Clark. Properties and detectability of rogue synthetic biology (SynBio) products in complex matrices. Engineer Research and Development Center (U.S.), September 2022. http://dx.doi.org/10.21079/11681/45345.

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Synthetic biology (SynBio) aims to rationally engineer or modify traits of an organism or integrate the behaviors of multiple organisms into a singular functional organism through advanced genetic engineering techniques. One objective of this research was to determine the environmental persistence of engineered DNA in the environment. To accomplish this goal, the environmental persistence of legacy engineered DNA building blocks were targeted that laid the foundation for SynBio product development and application giving rise to “post-use products.” These building blocks include genetic constructs such as cloning and expression vectors, promoter/terminator elements, selectable markers, reporter genes, and multi-cloning sites. Shotgun sequencing of total DNA from water samples of pristine sites was performed and resultant sequence data mined for frequency of legacy recombinant DNA signatures. Another objective was to understand the fate of a standardized contemporary synthetic genetic construct (SC) in the context of various chassis systems/genetic configurations representing different degrees of “genetic bioavailability” to the environmental landscape. These studies were carried out using microcosms representing different environmental matrices (soils, waters, wastewater treatment plant (WWTP) liquor) and employed a novel genetic reporter system based on volatile organic compounds (VOC) detection to assess proliferation and persistence of the SC in the matrix over time.
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Dawson, William O., and Moshe Bar-Joseph. Creating an Ally from an Adversary: Genetic Manipulation of Citrus Tristeza. United States Department of Agriculture, January 2004. http://dx.doi.org/10.32747/2004.7586540.bard.

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Citrus is one of the major agricultural crops common to Israel and the United States, important in terms of nutrition, foreign exchange, and employment. The economy of both citrus industries have been chronically plagued by diseases caused by Citrus tristeza virus (CTV). The short term solution until virus-resistant plants can be used is the use of mild strain cross-protection. We are custom designing "ideal" protecting viruses to immunize trees against severe isolates of CTV by purposely inoculating existing endangered trees and new plantings to be propagated as infected (protected) citrus budwood. We crossed the substantial technological hurdles necessary to accomplish this task which included developing an infectious cDNA clone which allows in vitro manipulation of the virus and methods to then infect citrus plants. We created a series of hybrids between decline-inducing and mild CTV strains, tested them in protoplasts, and are amplifying them to inoculate citrus trees for evaluation and mapping of disease determinants. We also extended this developed technology to begin engineering transient expression vectors based on CTV as tools for genetic improvement of tree crops, in this case citrus. Because of the long periods between genetic transformation and the ultimate assay of mature tree characteristics, there is a great need for an effective system that allows the expression or suppression of target genes in fruiting plants. Virus-based vectors will greatly expedite progress in citrus genetic improvement. We characterized several components of the virus that provides necessary information for designing virus-based vectors. We characterized the requirements of the 3 ’-nontranslated replication promoter and two 3 ’-ORF subgenomic (sg) mRNA controller elements. We discovered a novel type of 5’-terminal sgRNAs and characterized the cis-acting control element that also functions as a strong promoter of a 3 ’-sgRNA. We showed that the p23 gene controls negative-stranded RNA synthesis and expression of 3 ’ genes. We identified which genes are required for infection of plants, which are host range determinants, and which are not needed for plant infection. We continued the characterization of native dRNA populations and showed the presence of five different classes including class III dRNAs that consists of infectious and self-replicating molecules and class V dRNAs that contain all of the 3 ’ ORFs, along with class IV dRNAs that retain non-contiguous internal sequences. We have constructed and tested in protoplasts a series of expression vectors that will be described in this proposal.
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Zhang, Hongbin, Shahal Abbo, Weidong Chen, Amir Sherman, Dani Shtienberg, and Frederick Muehlbauer. Integrative Physical and Genetic Mapping of the Chickpea Genome for Fine Mapping and Analysis of Agronomic Traits. United States Department of Agriculture, March 2010. http://dx.doi.org/10.32747/2010.7592122.bard.

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Chickpea is the third most important pulse crop in the world and ranks first in the Middle East; however, it has been subjected to only limited research in modern genomics. In the first period of this project (US-3034-98R) we constructed two large-insert BAC and BIBAC libraries, developed 325 SSR markers and mapped QTLs controlling ascochyta blight resistance (ABR) and days to first flower (DTF). Nevertheless, the utilities of these tools and results in gene discovery and marker-assisted breeding are limited due to the absence of an essential platform. The goals of this period of the project were to use the resources and tools developed in the first period of the project to develop a BAC/BIBAC physical map for chickpea and using it to identify BAC/BIBACcontigs containing agronomic genes of interest, with an emphasis on ABR and DTF, and develop DNA markers suitable for marker-assisted breeding. Toward these goals, we proposed: 1) Fingerprint ~50,000 (10x) BACs from the BAC and BIBAC libraries, assemble the clones into a genome-wide BAC/BIBAC physical map, and integrate the BAC/BIBAC map with the existing chickpea genetic maps (Zhang, USA); 2) fine-map ABR and DTFQTLs and enhance molecular tools for chickpea genetics and breeding (Shahal, Sherman and DaniShtienberg, Israel; Chen and Muehlbauer; USA); and 3) integrate the BAC/BIBAC map with the existing chickpea genetic maps (Sherman, Israel; Zhang and Chen, USA). For these objectives, a total of $460,000 was requested originally, but a total of $300,000 was awarded to the project. We first developed two new BAC and BIBAC libraries, Chickpea-CME and Chickpea- CHV. The chickpea-CMEBAC library contains 22,272 clones, with an average insert size of 130 kb and equivalent to 4.0 fold of the chickpea genome. The chickpea-CHVBIBAC library contains 38,400 clones, with an average insert size of 140 kb and equivalent to 7.5 fold of the chickpea genome. The two new libraries (11.5 x), along with the two BAC (Chickpea-CHI) and BIBAC (Chickpea-CBV) libraries (7.1 x) constructed in the first period of the project, provide libraries essential for chickpea genome physical mapping and many other genomics researches. Using these four libraries we then developed the proposed BAC/BIBAC physical map of chickpea. A total of 67,584 clones were fingerprinted, and 64,211 (~11.6 x) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBACcontigs, with each containing an average of 39.2 clones and having an average physical length of 559 kb. The contigs collectively span ~1,088 Mb, being 1.49 fold of the 740- Mb chickpea genome. Third, we integrated the physical map with the two existing chickpea genetic maps using a total of 172 (124 + 48) SSR markers. Fourth, we identified tightly linked markers for ABR-QTL1, increased marker density at ABR-QTL2 and studied the genetic basis of resistance to pod abortion, a major problem in the east Mediterranean, caused by heat stress. Finally, we, using the integrated map, isolated the BAC/BIBACcontigs containing or closely linked to QTL4.1, QTL4.2 and QTL8 for ABR and QTL8 for DTF. The integrated BAC/BIBAC map resulted from the project will provide a powerful platform and tools essential for many aspects of advanced genomics and genetics research of this crop and related species. These includes, but are not limited to, targeted development of SNP, InDel and SSR markers, high-resolution mapping of the chickpea genome and its agronomic genes and QTLs, sequencing and decoding of all genes of the genome using the next-generation sequencing technology, and comparative genome analysis of chickpea versus other legumes. The DNA markers and BAC/BIBACcontigs containing or closely linked to ABR and DTF provide essential tools to develop SSR and SNP markers well-suited for marker-assisted breeding of the traits and clone their corresponding genes. The development of the tools and knowledge will thus promote enhanced and substantial genetic improvement of the crop and related legumes.
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Solvin, Thomas, and Inger Sundheim Fløistad. Statistics: Forest Seeds and Plants in the Nordic Region – Version 2023. The Nordic Genetic Resource Center (NordGen), August 2023. http://dx.doi.org/10.53780/qoub7866.

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The Nordic Genetic Resource Center (NordGen) is the joint genebank and knowledge center for genetic resources in the Nordic countries. Our mission is to conserve and promote the sustainable use of genetic diversity among animals, forests and plants that are important for Nordic agriculture and forestry. “Statistics: Forest Seeds and Plants in the Nordic Region – Version 2023” is the second edition in a biennial statistics report on forest seed and plant material in the Nordic countries. The first edition was published in 2021. This edition has been expanded by including more statistics and more species than the first report, as well as including more recent data from the years 2020 and 2021. The report compiles statistics and reports contributed by representatives of each country in the NordGen Forest Regeneration Council.
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Li, Li, Joseph Burger, Nurit Katzir, Yaakov Tadmor, Ari Schaffer, and Zhangjun Fei. Characterization of the Or regulatory network in melon for carotenoid biofortification in food crops. United States Department of Agriculture, April 2015. http://dx.doi.org/10.32747/2015.7594408.bard.

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The general goals of the BARD research grant US-4423-11 are to understand how Or regulates carotenoid accumulation and to reveal novel strategies for breeding agricultural crops with enhanced β-carotene level. The original objectives are: 1) to identify the genes and proteins in the Or regulatory network in melon; 2) to genetically and molecularly characterize the candidate genes; and 3) to define genetic and functional allelic variation of these genes in a representative germplasm collection of the C. melo species. Or was found by the US group to causes provitamin A accumulation in chromoplasts in cauliflower. Preliminary genetic study from the Israeli group revealed that the melon Or gene (CmOr) completely co-segregated with fruit flesh color in a segregating mapping population and in a wide melon germplasm collection, which set the stage for the funded research. Major conclusions and achievements include: 1). CmOris proved to be the gene that controls melon fruit flesh color and represents the previously described gflocus in melon. 2). Genetic and molecular analyses of CmOridentify and confirm a single SNP that is responsible for the orange and non-orange phenotypes in melon fruit. 3). Alteration of the evolutionarily conserved arginine in an OR protein to both histidine or alanine greatly enhances its ability to promote carotenoid accumulation. 4). OR promotes massive carotenoid accumulation due to its dual functions in regulating both chromoplast biogenesis and carotenoid biosynthesis. 5). A bulk segregant transcriptome (BSRseq) analysis identifies a list of genes associated with the CmOrregulatory network. 6). BSRseq is proved to be an effective approach for gene discovery. 7). Screening of an EMS mutation library identifies a low β mutant, which contains low level of carotenoids due to a mutation in CmOrto produce a truncated form of OR protein. 8). low β exhibits lower germination rate and slow growth under salt stress condition. 9). Postharvest storage of fruit enhances carotenoid accumulation, which is associated with chromoplast development. Our research uncovers the molecular mechanisms underlying the Or-regulated high level of carotenoid accumulation via regulating carotenoidbiosynthetic capacity and storage sink strength. The findings provide mechanistic insights into how carotenoid accumulation is controlled in plants. Our research also provides general and reliable molecular markers for melon-breeding programs to select orange varieties, and offers effective genetic tools for pro-vitamin A enrichment in other important crops via the rapidly developed genome editing technology. The newly discovered low β mutant could lead to a better understanding of the Or gene function and its association with stress response, which may explain the high conservation of the Or gene among various plant species.
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