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Relevant bibliographies by topics / Gene mapping

Academic literature on the topic 'Gene mapping'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 September 2023

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Contents

Journal articles
Dissertations / Theses
Books
Book chapters
Conference papers
Reports

Journal articles on the topic "Gene mapping":

1

Lathrop, Gregory M., Dora Cherif, Cécile Julier, and Michael James. "Gene mapping." Current Opinion in Biotechnology 1, no. 2 (December 1990): 172–79. http://dx.doi.org/10.1016/0958-1669(90)90027-i.

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Ehrhart, Friederike, Jonathan Melius, Elisa Cirillo, Martina Kutmon, Egon L. Willighagen, Susan L. Coort, Leopold M. G. Curfs, and Chris T. Evelo. "Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services." F1000Research 7 (September 3, 2018): 1390. http://dx.doi.org/10.12688/f1000research.15708.1.

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Database identifier mapping services are important to make database information interoperable. BridgeDb offers such a service. Available mapping for BridgeDb link 1. genes and gene products identifiers, 2. metabolite identifiers and InChI structure description, and 3. identifiers for biochemical reactions and interactions between multiple resources that use such IDs while the mappings are obtained from multiple sources. In this study we created BridgeDb mapping databases for selections of genes-to-variants (and variants-to-genes) based on the variants described in Ensembl. Moreover, we demonstrated the use of these mappings in different software tools like R, PathVisio, Cytoscape and a local installation using Docker. The variant mapping databases are now described on the BridgeDb website and are available from the BridgeDb mapping database repository and updated according to the regular BridgeDb mapping update schedule.

3

Frézal, Jean. "Genes, gene map, gene mapping." Cytogenetic and Genome Research 46, no. 1-4 (1987): 1–10. http://dx.doi.org/10.1159/000132469.

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Harrap, Stephen B. "Repetitive gene mapping." Journal of Hypertension 13, no. 5 (May 1995): 567. http://dx.doi.org/10.1097/00004872-199505000-00013.

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Stern, Victoria. "Mapping the Spine, Gene by Gene." Scientific American Mind 19, no. 5 (October 2008): 8. http://dx.doi.org/10.1038/scientificamericanmind1008-8a.

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Daniels, D. L., and F. R. Blattner. "Mapping using gene encyclopaedias." Nature 325, no. 6107 (February 1987): 831–32. http://dx.doi.org/10.1038/325831a0.

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Harper, P. S. "Gene mapping and neurogenetics." Journal of Medical Genetics 24, no. 9 (September 1, 1987): 513–14. http://dx.doi.org/10.1136/jmg.24.9.513.

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Harper, P. S. "Human Gene Mapping 9." Journal of Medical Genetics 25, no. 11 (November 1, 1988): 788. http://dx.doi.org/10.1136/jmg.25.11.788.

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Yates, J. R. W. "Human Gene Mapping 10." Journal of Medical Genetics 27, no. 5 (May 1, 1990): 343. http://dx.doi.org/10.1136/jmg.27.5.343-a.

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SYKES, BRYAN. "Mapping Collagen Gene Mutations." Annals of the New York Academy of Sciences 580, no. 1 Structure, Mo (February 1990): 385–89. http://dx.doi.org/10.1111/j.1749-6632.1990.tb17946.x.

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Dissertations / Theses on the topic "Gene mapping":

1

Audetat, Katherine. "Mapping the mop3 gene." Thesis, The University of Arizona, 2009. http://hdl.handle.net/10150/192275.

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Malik, Sajid Perwaiz. "Gene mapping in syndactyly families." [S.l.] : [s.n.], 2005. http://archiv.ub.uni-marburg.de/diss/z2005/0262/.

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Backström, Niclas. "Gene Mapping in Ficedula Flycatchers." Doctoral thesis, Uppsala universitet, Institutionen för evolution, genomik och systematik, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9513.

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In order to get full understanding of how evolution proceeds in natural settings it is necessary to reveal the genetic basis of the phenotypic traits that play a role for individual fitness in different environments. There are a few possible approaches, most of which stem from traditional mapping efforts in domestic animals and other model species. Here we set the stage for gene mapping in natural populations of birds by producing a large number of anchor markers of broad utility for avian genetical research and use these markers to generate a genetic map of the collared flycatcher (Ficedula albicollis). The map reveals a very high degree of synteny and gene order conservation between bird species separated by as much as 100 million years. This is encouraging for later stages of mapping procedures in natural populations since this means that there is a possibility to use the information from already characterized avian genomes to track candidate genes for detailed analysis in non-model species. One interesting aspect of the low degree of rearrangements occurring in the avian genomes is that this could play a role in the low rate of hybridization barriers formed in birds compared to for instance mammals. An analysis of Z-linked gene markers reveals relatively long-range linkage disequilibrium (LD) in collared flycatchers compared to other outbred species but still, LD seems to decay within < 50 kb indicating that > 20.000 markers would be needed to cover the genome in an association scan. A detailed scan of 74 Z-linked genes evenly distributed along the chromosome in both the collared flycatcher and the pied flycatcher (Ficedula hypoleuca) indicates that there are regions that evolve under directional selection, regions that might harbor loci of importance for adaptive divergence and/or hybrid inviability.

4

Söderhäll, Cilla. "Gene mapping of atopic dermatitis /." Stockholm : [Karolinska institutets bibl.], 2001. http://diss.kib.ki.se/2001/91-7349-088-1/.

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Setakis, Efrosini. "Gene mapping using DNA pools." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615651.

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Bryant, Stephen Paul. "Pedigree analysis and gene mapping." Thesis, Open University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390811.

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Hernandez-Sanchez, Jules. "Gene mapping using linkage disequilibrium." Thesis, University of Edinburgh, 2002. http://hdl.handle.net/1842/14058.

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The power of QTL detection was studied both empirically and deterministically for several methods. TDT was more powerful than a linkage test, but less powerful than a pure association test. There were no great differences in power between TDTs. One of the TDTs was implemented in BLUP (Best Linear Unbiased Prediction) to study the effect of a candidate gene, the melanocortin 4- receptor (MC4R), on growth, appetite and fatness in pigs. We found significant effects on growth and fatness but not on appetite. TDT uses within families genetic variation. A novel parameter to estimate gene effects using between families genetic variation was also included. If there is no spurious disequilibrium both estimates should be identical, otherwise only the within-families estimator is unbiased. It was more powerful to simulate missing parental genotypes with Gibbs Sampling than analysing data with sib-ship TDTs disregarding parental information. TDT was also used in a genome-wide search for markers associated with bovine spongiform encaphalopathy (BSE). TDT was implemented using logistic regressions, more amenable to statistical modelling than the original form. Maker loci near the Prion Protein gene did not show any associations with BSE, however, markers located on chromosomes 5, 10 and 20, did. A second study that focused on these three chromosomal regions confirmed the association for the marker on chromosome 5. TDT has shown reasonable power and exceptional robustness when mapping QTL in structured populations. Therefore TDT should be part of the gene cartographers’ continuously evolving arsenal of tools for gene mapping. However, previously published TDTs were developed for analysing human populations, whereas domestic/wild populations have different structures and histories that may require alternative statistical analyses. Linked gene flow (LGF) theory can be used for predicting identity-by-descent (IBD) probabilities between individuals. IBD probabilities are at the core of mixed model equations for mapping QTL in outbred populations via variance components estimation. In this thesis, LGF theory was used for determining inbreeding within each individual and chromosomal location using multi-marker information, hence paving the way for further developments.

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Korn, Richard Mervyn. "Mapping sex determining genes and development of techniques for gene mapping in the domestic fowl." Thesis, University of Cambridge, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624653.

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Fasulo, Daniel. "Algorithms for DNA restriction mapping /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/7020.

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Tell, Désirée von. "Welander distal myopathy : gene mapping and analysis of candidate genes /." Stockholm, 2004. http://diss.kib.ki.se/2003/91-7349-764-9.

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Books on the topic "Gene mapping":

1

Helsinki), International Workshop on Human Gene Mapping (8th 1985 University of. Human gene mapping 8. Basel: Karger, 1985.

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2

Helsinki), International Workshop on Human Gene Mapping (8th 1985. Human gene mapping 8. Basel: Karger, 1985.

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3

B, Schook Lawrence, Lewin Harris Alan, and McLaren David G, eds. Gene-mapping techniques and applications. New York: Marcel Dekker, 1991.

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4

Boultwood, Jacqueline. Gene Isolation and Mapping Protocols. New Jersey: Humana Press, 1996. http://dx.doi.org/10.1385/0896034828.

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Minou, Bina. Gene Mapping, Discovery, and Expression. New Jersey: Humana Press, 2006. http://dx.doi.org/10.1385/1597450979.

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Robinson, Roy. Gene Mapping in Laboratory Mammals. Boston, MA: Springer US, 1995. http://dx.doi.org/10.1007/978-1-4684-2982-4.

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7

Workshop on Human Gene Mapping (1987 Santa Fe, N.M.). Workshop on Human Gene Mapping. Washington: U.S. G.P.O., 1988.

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8

Jacqueline, Boultwood, ed. Gene isolation and mapping protocols. Totowa, N.J: Humana Press, 1997.

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9

National Cancer Institute (U.S.), ed. Understanding gene testing. [Bethesda, Md.]: U.S. Dept. of Health and Human Services, Public Health Service, National Institutes of Health, National Cancer Institute, 1997.

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10

J, Harwood Adrian, ed. Protocols for gene analysis. Totowa, N.J: Humana Press, 1994.

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Book chapters on the topic "Gene mapping":

1

Nahler, Gerhard. "gene mapping." In Dictionary of Pharmaceutical Medicine, 78. Vienna: Springer Vienna, 2009. http://dx.doi.org/10.1007/978-3-211-89836-9_587.

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2

Guenet, Jean-Louis, Fernando Benavides, Jean-Jacques Panthier, and Xavier Montagutelli. "Gene Mapping." In Genetics of the Mouse, 89–125. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-662-44287-6_4.

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3

Williamson, Robert. "Human Gene Mapping." In Ciba Foundation Symposium 130 - Molecular Approaches to Human Polygenic Disease, 3–13. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470513507.ch2.

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4

Carlberg, Carsten, and Ferdinand Molnár. "Mapping the Genome." In Mechanisms of Gene Regulation, 109–25. Dordrecht: Springer Netherlands, 2016. http://dx.doi.org/10.1007/978-94-017-7741-4_7.

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Carlberg, Carsten, and Ferdinand Molnár. "Mapping the Genome." In Mechanisms of Gene Regulation, 105–21. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-7905-1_7.

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6

Causse, Mathilde, and Silvana Grandillo. "Gene Mapping in Tomato." In Compendium of Plant Genomes, 23–37. Berlin, Heidelberg: Springer Berlin Heidelberg, 2016. http://dx.doi.org/10.1007/978-3-662-53389-5_3.

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7

Saddique, Muhammad Abu Bakar, Zulfiqar Ali, Muhammad Ali Sher, Babar Farid, Furqan Ahmad, and Sarmad Frogh Arshad. "Gene Mapping in Cotton." In Cotton Breeding and Biotechnology, 69–85. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9781003096856-5.

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Hu, Zhaoguang, Jian Zhang, and Ning Zhang. "Economic Gene Mapping of China." In China’s Economic Gene Mutations, 91–140. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-47298-9_3.

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Housman, David E., and David L. Nelson. "Use of Metaphase-Chromosome Transfer for Mammalian Gene Mapping." In Gene Transfer, 95–115. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4684-5167-2_4.

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Maizels, Leonid, and Lior Gepstein. "Electrophysiological Implications of Myocardial Cell and Gene Therapy Strategies." In Cardiac Mapping, 732–41. Oxford, UK: Wiley-Blackwell, 2012. http://dx.doi.org/10.1002/9781118481585.ch68.

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Conference papers on the topic "Gene mapping":

1

Huber, P., J. Dalmon, M. Laurent, G. Courtois, D. Thevenon, and G. Marguerie. "CHARACTERIZATION OFTHE 5’FLANKING REGION FOR THE HUMAN FIBRINOGEN β GENE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642889.

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Fibrinogen is coded by three separate genes located in a 50kb region of chromosome 4 and organized in a α - β - γ orientation with an inversion of the gene 3- A human genomic library was constructed using the EMBL4 phage and screened with cDNA probes coding for human fibrinogen Aα, Bβ and γ chains. Clones, covering the fibrinogen locus,were identified, and their organization was analyzed by means of hybridization and restriction mapping. Among these clones one recombinant phage containing the β gene and large 5’ and 3’ -flanking sequences was isolated.To identify the regulatory sequences Dpstream from the human β gene, a 1.5 kb fragment of the immediate 5’-flanking region was sequenced. The SI mapping experiments revealed three transcription initiation sites. PotentialTATA and CAAT sequences were identified upstream the initiation start points at the positions -21 and -58 from the first initiation start point.Comparison of this sequence with that previously reported for the same region upstream from the human γ gene revealed no significant homology which suggests that the potential promoting sequences of these genes are different. In contrast, comparison of the 5’flanking regions of human and rat β genes showed more than 80% homology for 142 bp upstream from the gene. This highly conserved region is a potential candidate for a regulatory sequence of the human β gene.To verify this activity, a β fibrinogen minigene was constructed by deletion of the internal part of the normal gene and including 3.4kb of the 5’flanking region and 1.4kb of the 3’flanking region. The minigene was transfected into HepG2, a human hepatoma cell line, to show whether the 5’flanking region of the human fibrinogen gene contains DNA sequences sufficient for efficient transcription in HepG2. Constructions of several parts of the sequenced 5’flanking region of the human β gene with the gene of the chloramphenical acetyl transferase have been also transfected in the HepG2 cells to determine the specificity of the gene expression and to localize the sequences controlling the transcription of the gene.

2

Walhout, A. J. Marian. "GENE-CENTERED PROTEIN-DNA INTERACTOME MAPPING." In Proceedings of the CSB 2007 Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2007. http://dx.doi.org/10.1142/9781860948732_0006.

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Yu, Hao, I.-Hsin Chung, and Jose Moreira. "Blue Gene system software---Topology mapping for Blue Gene/L supercomputer." In the 2006 ACM/IEEE conference. New York, New York, USA: ACM Press, 2006. http://dx.doi.org/10.1145/1188455.1188576.

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Zhao, Guoyi, Li Guo, Lixin Gao, and Li-Jun Ma. "Inferring regulatory networks through orthologous gene mapping." In 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2013. http://dx.doi.org/10.1109/bibm.2013.6732739.

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Chen, Yidong, Harry Hung-I. Chen, and Yufei Huang. "Mapping miRNA Regulation to Functional Gene Sets." In 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing. IEEE, 2009. http://dx.doi.org/10.1109/ijcbs.2009.64.

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DE LA VEGA, F. M., K. K. KIDD, and A. COLLINS. "COMPUTATIONAL TOOLS FOR COMPLEX TRAIT GENE MAPPING." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2003. http://dx.doi.org/10.1142/9789812704856_0009.

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Yu, Hao, I.-hsin Chung, and Jose Moreira. "Topology Mapping for Blue Gene/L Supercomputer." In ACM/IEEE SC 2006 Conference (SC'06). IEEE, 2006. http://dx.doi.org/10.1109/sc.2006.63.

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Cool, D. E., and R. T. A. MacGillivray. "CHARACTERIZATION OF THe HUMAN FACTOR XII GENE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642800.

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Surface activation of the plasma systems involved with coagulation, fibrinolysis, renin formation and kinin generation involves factor XII (Hageman factor). This protein is a 76,000 dalton glycoprotein which circulates in plasma as an inactive form of a serine protease. A human liver cDNA coding for factor XII was used to screen a human genomic phage library. Two overlapping clones were isolated, XHXII27 and XHXII76, and contain the entire gene for human factor XII. The gene is 13.5 Kbp in length and consists of 14 exons and 13 introns. The transcriptional start site of the mRNA was determined using S1 mapping and primer extension analysis. The results indicate that the 5′ untranslated end of the mRNA has a leader sequence of 47 bp and is not interrupted by an intron in the gene. DNA sequence analysis of the region upstream of the transcriptional start site does not contain TATA or CAAT sequences, which are often found in other genes transcribed by RNA polymerase II. The positions of the introns in the coding sequence separate the protein into domains which are homologous to similar regions found in fibronectin and tissue-type plasminogen activator. Furthermore, wherever protein homologies are found, the positions of the introns in the triplet codon occur in the same reading frame as in the tissue-type plasminogen activator, urokinase plasminogen activator and factor XII genes. The intron/exon organization of the factor XII gene is different to the organization of other coagulation genes such as prothrombin, factor IX and factor X. Therefore, factor XII appears to have evolved as a member of the plasminogen activator family of genes rather than as a member of the clotting factor gene family.

9

Liu, Qiang, and Haiyun Li. "Selection of PD Genes from Multiplex Three-Dimensional Brain Gene Expression Mapping." In 2007 1st International Conference on Bioinformatics and Biomedical Engineering. IEEE, 2007. http://dx.doi.org/10.1109/icbbe.2007.59.

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Liang, Victor C., and Vincent T. Y. Ng. "Alternative Feature Mapping for Heterogeneous Gene Data Classification." In 2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering (BIBE). IEEE, 2009. http://dx.doi.org/10.1109/bibe.2009.21.

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Reports on the topic "Gene mapping":

1

Davis, Arthur. Mapping of a Breast Carcinoma Tumor Suppressor Gene to Chromosome 11p15.5. Fort Belvoir, VA: Defense Technical Information Center, January 1999. http://dx.doi.org/10.21236/ada371061.

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2

Moore, Tracey. Mapping of a Breast Carcinoma Tumor Suppressor Gene to Chromosome 11P15.5. Fort Belvoir, VA: Defense Technical Information Center, July 1997. http://dx.doi.org/10.21236/ada330191.

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Moore, Tracy. Mapping of a Breast Carcinoma Tumor Suppressor Gene to Chromosome 11p15.5. Fort Belvoir, VA: Defense Technical Information Center, July 1996. http://dx.doi.org/10.21236/ada315709.

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4

Zamir, Dani, Steven Tanksley, and Robert Fluhr. Cloning a Fusarium Resistance Gene in Tomato Based on Knowledge of its Map Position. United States Department of Agriculture, July 1995. http://dx.doi.org/10.32747/1995.7604934.bard.

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The objectives of this project were to develop the tools and methodologies for positional cloning of genes in tomato and apply them for the cloning a Fusarium resistance gene - I2.. The feasibility of positional cloning of disease resistance genes was demonstrated for Pto which confers resistance to pseudomonas (Martin et al. 1993). The Fusarium resistance gene was mapped genetically and physically and was found to be in close proximity to TG 105 (Segal et al. 1992). To obtain fine mapping of gene I2, and additional target genes in future projects, a high density linkage map was developed (Tanksley et al. 1992; Broun and Tanksley 1993). In addition two permanent mapping populations were constructed: a recombinant inbred (Paran et al. 1995; Zamir et al. 1993) and an introgression line population (Eshed et al. 1992; Eshed and Zamir 1994). Using these resources we determined that the I2 locus shows complete co-segregation, down to a resolution of a few Kb, with SL8 which shows architectural similarity with other plant resistance genes. Transformation and complementation analysis is in progress (Ori et al. in preparation).

5

Hammel, Kenneth E., John Ralph, Christopher G. Hunt, and Carl J. Houtman. Fungal Biodegradative Oxidants in Lignocellulose: Fluorescence Mapping and Correlation With Gene Expression. Office of Scientific and Technical Information (OSTI), September 2016. http://dx.doi.org/10.2172/1319808.

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Savaldi-Goldstein, Sigal, and Todd C. Mockler. Precise Mapping of Growth Hormone Effects by Cell-Specific Gene Activation Response. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7699849.bard.

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Plant yield largely depends on a complex interplay and feedback mechanisms of distinct hormonal pathways. Over the past decade great progress has been made in elucidating the global molecular mechanisms by which each hormone is produced and perceived. However, our knowledge of how interactions between hormonal pathways are spatially and temporally regulated remains rudimentary. For example, we have demonstrated that although the BR receptor BRI1 is widely expressed, the perception of BRs in epidermal cells is sufficient to control whole-organ growth. Supported by additional recent works, it is apparent that hormones are acting in selected cells of the plant body to regulate organ growth, and furthermore, that local cell-cell communication is an important mechanism. In this proposal our goals were to identify the global profile of translated genes in response to BR stimulation and depletion in specific tissues in Arabidopsis; determine the spatio-temporal dependency of BR response on auxin transport and signaling and construct an interactive public website that will provide an integrated analysis of the data set. Our technology incorporated cell-specific polysome isolation and sequencing using the Solexa technology. In the first aim, we generated and confirmed the specificity of novel transgenic lines expressing tagged ribosomal protein in various cell types in the Arabidopsis primary root. We next crossed these lines to lines with targeted expression of BRI1 in the bri1 background. All lines were treated with BRs for two time points. The RNA-seq of their corresponding immunopurified polysomal RNA is nearly completed and the bioinformatic analysis of the data set will be completed this year. Followed, we will construct an interactive public website (our third aim). In the second aim we started revealing how spatio-temporalBR activity impinges on auxin transport in the Arabidopsis primary root. We discovered the unexpected role of BRs in controlling the expression of specific auxin efflux carriers, post-transcriptionally (Hacham et al, 2012). We also showed that this regulation depends on the specific expression of BRI1 in the epidermis. This complex and long term effect of BRs on auxin transport led us to focus on high resolution analysis of the BR signaling per se. Taking together, our ongoing collaboration and synergistic expertise (hormone action and plant development (IL) and whole-genome scale data analysis (US)) enabled the establishment of a powerful system that will tell us how distinct cell types respond to local and systemic BR signal. BR research is of special agriculture importance since BR application and BR genetic modification have been shown to significantly increase crop yield and to play an important role in plant thermotolerance. Hence, our integrated dataset is valuable for improving crop traits without unwanted impairment of unrelated pathways, for example, establishing semi-dwarf stature to allow increased yield in high planting density, inducing erect leaves for better light capture and consequent biomass increase and plant resistance to abiotic stresses.

7

Paran, Ilan, and Molly Jahn. Genetics and comparative molecular mapping of biochemical and morphological fruit characters in Capsicum. United States Department of Agriculture, March 2005. http://dx.doi.org/10.32747/2005.7586545.bard.

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Original objectives: The overall goal of our work was to gain information regarding the genetic and molecular control of pathways leading to the production of secondary metabolites determining major fruit quality traits in pepper and to develop tools based on this information to assist in crop improvement. The specific objectives were to: (1) Generate a molecular map of pepper based on simple sequence repeat (SSR) markers. (2) Map QTL for capsaicinoid (pungency) content (3) Determine possible association between capsaicinoid and carotenoid content and structural genes for capsaicinoid and carotenoid biosynthesis. (4) Map QTL for quantitative traits controlling additional fruit traits. (5) Map fruit-specific ESTs and determine possible association with fruit QTL (6) Map the C locus that determines the presence and absence of capsaicinoid in pepper fruit and identify candidate genes for C.locus. Background: Pungency, color, fruit shape and fruit size are among the most important fruit quality characteristics of pepper. Despite the importance of the pepper crop both in the USA and Israel, the genetic basis of these traits was poorly understood prior to the studies conducted in the present proposal. In addition, molecular tools for use in pepper improvement were lacking. Major conclusions and achievements: Our studies enabled the development of a saturated genetic map of pepper that includes numerous SSR markers. This map has been integrated with a number of other independent maps resulting in the publication of a single resource map consisting of more than 2000 markers. Unlike previous maps based primarily on tomato-originated RFLP markers, the new maps are based on PCR markers that originate in Capsicum providing a comprehensive and versatile resource for marker-assisted selection in pepper. We determined the genetic and molecular bases of qualitative and quantitative variation of pungency, a character unique to pepper fruit. We mapped and subsequently cloned the Pun1 gene that serves as a master regulatoar for capsaicinoid accumulation and showed that it is an acyltransferase. By sequencing the Pun1 gene in pungent and non-pungent cultivars we identified a deletion that abolishes the expression of the gene in the latter cultivars. We also identified QTL that control capsaicinoid content and therefore pungency level. These genes will allow pepper breeders to manipulate the level of pungency for specific agricultural and industrial purposes. In addition to pungency we identified genes and QTL that control other key developmental processes of fruit development such as color, texture and fruit shape. The A gene controlling anthocyanin accumulation in the immature fruit was found as the ortholog of the petunia transcription factor Anthocyanin2. The S gene required for the soft flesh and deciduous fruit nature typical of wild peppers was identified as the ortholog of tomato polygalacturonase. We identified two major QTL controlling fruit shape, fs3.1 and fs10.1, that differentiate elongated and blocky and round fruit shapes, respectively. Scientific and agricultural implications: Our studies allowed significant advances in our understanding of important processes of pepper fruit development including the isolation and characterization of several well known genes. These results also provided the basis for the development of molecular tools that can be implemented for pepper improvement. A total of eleven refereed publications have resulted from this work, and several more are in preparation.

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Levin, Ilan, John W. Scott, Moshe Lapidot, and Moshe Reuveni. Fine mapping, functional analysis and pyramiding of genes controlling begomovirus resistance in tomato. United States Department of Agriculture, November 2014. http://dx.doi.org/10.32747/2014.7594406.bard.

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Abstract. Tomato yellow leaf curl virus (TYLCV), a monopartitebegomovirus, is one of the most devastating viruses of cultivated tomatoes and poses increasing threat to tomato production worldwide. Because all accessions of the cultivated tomato are susceptible to these viruses, wild tomato species have become a valuable resource of resistance genes. QTL controlling resistance to TYLCV and other begomoviruses (Ty loci) were introgressed from several wild tomato species and mapped to the tomato genome. Additionally, a non-isogenic F₁diallel study demonstrated that several of these resistance sources may interact with each other, and in some cases generate hybrid plants displaying lower symptoms and higher fruit yield compared to their parental lines, while their respective resistance genes are not necessarily allelic. This suggests that pyramiding genes originating from different resistance sources can be effective in obtaining lines and cultivars which are highly resistant to begomoviruses. Molecular tools needed to test this hypothesis have been developed by our labs and can thus significantly improve our understanding of the mechanisms of begomovirus resistance and how to efficiently exploit them to develop wider and more durable resistance. Five non-allelic Ty loci with relatively major effects have been mapped to the tomato genome using molecular DNA markers, thereby establishing tools for efficient marker assisted selection, pyramiding of multiple genes, and map based gene cloning: Ty-1, Ty-2, Ty-3, Ty-4, and ty-5. This research focused on Ty-3 and Ty-4 due to their broad range of resistance to different begomoviruses, including ToMoV, and on ty-5 due to its exceptionally high level of resistance to TYLCV and other begomoviruses. Our aims were: (1) clone Ty-3, and fine map Ty-4 and Ty-5 genes, (2)introgress each gene into two backgroundsand develop semi isogenic lines harboring all possible combinations of the three genes while minimizing linkage-drag, (3) test the resulting lines, and F₁ hybrids made with them, for symptom severity and yield components, and (4) identify and functionally characterize candidate genes that map to chromosomal segments which harbor the resistance loci. During the course of this research we have: (1) found that the allelic Ty-1 and Ty-3 represent two alternative alleles of the gene coding DFDGD-RDRP; (2) found that ty-5is highly likely encoded by the messenger RNA surveillance factor PELOTA (validation is at progress with positive results); (3) continued the map-based cloning of Ty-4; (4) generated all possible gene combinations among Ty-1, Ty-3 and ty-5, including their F₁ counterparts, and tested them for TYLCV and ToMoV resistance; (5) found that the symptomless line TY172, carrying ty-5, also carries a novel allele of Ty-1 (termed Ty-1ⱽ). The main scientific and agricultural implications of this research are as follows: (1) We have developed recombination free DNA markers that will substantially facilitate the introgression of Ty-1, Ty-3 and ty-5 as well as their combinations; (2) We have identified the genes controlling TYLCV resistance at the Ty-1/Ty-3 and ty-5 loci, thus enabling an in-depth analyses of the mechanisms that facilitate begomovirus resistance; (3) Pyramiding of Ty resistance loci is highly effective in providing significantly higher TYLCV resistance.

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Belanger, Faith, Nativ Dudai, and Nurit Katzir. Genetic Linkage Mapping of Basil (Ocimum basilicum). United States Department of Agriculture, March 2010. http://dx.doi.org/10.32747/2010.7593385.bard.

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The ultimate goal of this project is to develop a genetic linkage map of basil (Ocimumbasilicum). We received 1 year of funding from BARD to conduct a feasibility study. Below is a summary of our study. During this year we evaluated the cultivars ‘Perrie’ and ‘Cardinal’ for DNA sequence polymorphisms using AFLPs and gene-based markers. We evaluated an F2 population for variation in production of volatile compounds. We also determined the nuclear DNA content of 8 species of Ocimum. All of this information will be useful in the future for genetic linkage mapping of basil.

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Breiman, Adina, Jan Dvorak, Abraham Korol, and Eduard Akhunov. Population Genomics and Association Mapping of Disease Resistance Genes in Israeli Populations of Wild Relatives of Wheat, Triticum dicoccoides and Aegilops speltoides. United States Department of Agriculture, December 2011. http://dx.doi.org/10.32747/2011.7697121.bard.

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Wheat is the most widely grown crop on earth, together with rice it is second to maize in total global tonnage. One of the emerging threats to wheat is stripe (yellow) rust, especially in North Africa, West and Central Asia and North America. The most efficient way to control plant diseases is to introduce disease resistant genes. However, the pathogens can overcome rapidly the effectiveness of these genes when they are wildly used. Therefore, there is a constant need to find new resistance genes to replace the non-effective genes. The resistance gene pool in the cultivated wheat is depleted and there is a need to find new genes in the wild relative of wheat. Wild emmer (Triticum dicoccoides) the progenitor of the cultivated wheat can serve as valuable gene pool for breeding for disease resistance. Transferring of novel genes into elite cultivars is highly facilitated by the availability of information of their chromosomal location. Therefore, our goals in this study was to find stripe rust resistant and susceptible genotypes in Israeli T. dicoccoides population, genotype them using state of the art genotyping methods and to find association between genetic markers and stripe rust resistance. We have screened 129 accessions from our collection of wild emmer wheat for resistance to three isolates of stripe rust. About 30% of the accessions were resistant to one or more isolates, 50% susceptible, and the rest displayed intermediate response. The accessions were genotyped with Illumina'sInfinium assay which consists of 9K single nucleotide polymorphism (SNP) markers. About 13% (1179) of the SNPs were polymorphic in the wild emmer population. Cluster analysis based on SNP diversity has shown that there are two main groups in the wild population. A big cluster probably belongs to the Horanum ssp. and a small cluster of the Judaicum ssp. In order to avoid population structure bias, the Judaicum spp. was removed from the association analysis. In the remaining group of genotypes, linkage disequilibrium (LD) measured along the chromosomes decayed rapidly within one centimorgan. This is the first time when such analysis is conducted on a genome wide level in wild emmer. Such a rapid decay in LD level, quite unexpected for a selfer, was not observed in cultivated wheat collection. It indicates that wild emmer populations are highly suitable for association studies yielding a better resolution than association studies in cultivated wheat or genetic mapping in bi-parental populations. Significant association was found between an SNP marker located in the distal region of chromosome arm 1BL and resistance to one of the isolates. This region is not known in the literature to bear a stripe rust resistance gene. Therefore, there may be a new stripe rust resistance gene in this locus. With the current fast increase of wheat genome sequence data, genome wide association analysis becomes a feasible task and efficient strategy for searching novel genes in wild emmer wheat. In this study, we have shown that the wild emmer gene pool is a valuable source for new stripe rust resistance genes that can protect the cultivated wheat.