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United States Department of Agriculture

Agricultural Research Service

Douglas Senalik
Vegetable Crops Research Unit
Horticulturist

Phone: (608) 262-7407
Fax: (608) 262-4743
USDA-ARS, VEGETABLE CROPS RESEARCH UNIT
1575 LINDEN DRIVE
MADISON, WI, 53706


Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Phylogenomics of the carrot genus (Daucus, Apiaceae) Reprint Icon - (Peer Reviewed Journal)
Arbizu, C., Ruess, H.M., Senalik, D.A., Simon, P.W., Spooner, D.M. 2014. Phylogenomics of the carrot genus (Daucus, Apiaceae). American Journal of Botany. 101(10):1666-1685.
Integrated molecular and morphological studies of Daucus - (Abstract Only)
Arbizu, C., Ruess, H.M., Senalik, D.A., Simon, P.W., Spooner, D.M. 2014. Integrated molecular and morphological studies of Daucus [abstract]. Botany. Paper No. 172.
Mechanisms of decreasing dysploidy in Cucumis - (Abstract Only)
Yang, L., Koo, D., Li, D., Jiang, J., Luan, F., Renner, S.S., Henaff, E., Sanseverino, W., Garcia-Mas, J., Casacuberta, J., Senalik, D.A., Simon, P.W., Chen, J., Weng, Y. 2014. Mechanisms of decreasing dysploidy in Cucumis [abstract]. Plant and Animal Genome Conference. Paper No. W233.
Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers Reprint Icon - (Peer Reviewed Journal)
Grzebelus, D., Iorizzo, M., Senalik, D.A., Ellison, S., Cavagnaro, P., Macko-Podgorni, A., Heller-Uszynska, K., Kilian, A., Nothnagel, T., Allender, C., Simon, P.W., Baranski, R. 2014. Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers . Molecular Breeding. 33(3):625-637.
Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis Reprint Icon - (Peer Reviewed Journal)
Yang, L., Koo, D., Li, D., Zhang, T., Jiang, J., Luan, F., Renner, S.S., Henaff, E., Sanseverino, W., Garcia-Mas, J., Senalik, D.A., Simon, P.W., Weng, Y., et al. 2014. Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis. Plant Journal. 77(1):16-30.
Multiple nuclear ortholog next generation sequencing phylogeny of Daucus - (Abstract Only)
Arbizu, C., Ruess, H.M., Senalik, D.A., Simon, P.W., Spooner, D.M. 2013. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus [abstract]. 36th International Carrot Conference. Paper. No. P16.
Multiple nuclear ortholog next generation sequencing phylogeny of Daucus - (Abstract Only)
Arbizu, C., Ruess, H.M., Senalik, D.A., Simon, P.W., Spooner, D.M. 2013. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus [abstract]. International Carrot Conference. Paper No. 17.
Genetic structure and domestication of carrot (Daucus carota subsp. sativus L.) (Apiaceae) - (Abstract Only)
Iorizzo, M., Senalik, D.A., Ellison, S.L., Grzebelus, D., Cavagnaro, P.F., Allender, C., Brunet, J., Spooner, D.M., Van Deynze, A., Simon, P.W. 2013. Genetic structure and domestication of carrot (Daucus carota subsp. sativus L.) (Apiaceae) [abstract]. Botanical Society of America Abstracts. Paper No. 654.
Multiple nuclear ortholog next generation sequencing phylogeny of Daucus - (Abstract Only)
Arbizu, C., Ruess, H.M., Senalik, D.A., Simon, P.W., Spooner, D.M. 2013. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus [abstract]. Botanical Society of America Abstracts. Paper No. 895.
Genetic structure and domestication of carrot (Daucus carota subsp. sativus)(Apiaceae) Reprint Icon - (Peer Reviewed Journal)
Iorizzo, M., Senalik, D.A., Ellison, S., Grzebelus, D., Cavagnaro, P., Allender, C., Brunet, J., Spooner, D.M., Van Deynze, A., Simon, P.W. 2013. Genetic structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae). American Journal of Botany. 100(5):930-938.
Against the traffic: The first evidence for mitochondrial DNA transfer into the plastid genome Reprint Icon - (Peer Reviewed Journal)
Iorizzo, M., Grzebelus, D., Senalik, D.A., Szklarczyk, M., Spooner, D.M., Simon, P.W. 2012. Against the traffic: The first evidence for mitochondrial DNA transfer into the plastid genome. Mobile Genetic Elements. 2(6):261-266.
Development of a high-throughput SNP resource to advance genomic, genetic and breeding research in carrot (Daucus carota L.) - (Abstract Only)
Iorizzo, M., Senalik, D.A., Ellison, S.L., Grzebelus, D., Cavagnaro, P., Spooner, D.M., Van Deynze, A., Simon, P.W. 2013. Development of a high-throughput SNP resource to advance genomic, genetic and breeding research in carrot (Daucus carota L.) [abstract]. Plant and Animal Genome Conference. Paper No. P0762.
Genome-wide association of the domestication syndrome in carrot (Daucus carota L.) - (Abstract Only)
Ellison, S.L., Iorizzo, M., Senalik, D.A., Simon, P.W. 2013. Genome-wide association of the domestication syndrome in carrot (Daucus carota L.) [abstract]. Plant and Animal Genome Conference. Paper No. P0698.
Diversity Arrays Technology (DArT) platform for genotyping and mapping in carrot (Daucus carota L.) - (Abstract Only)
Grzebelus, D., Baranski, R., Iorizzo, M., Senalik, D.A., Ellison, S.L., Cavagnaro, P., Macko-Podgorni, A., Heller-Uszynska, K., Kilian, A., Simon, P.W. 2013. Diversity Arrays Technology (DArT) platform for genotyping and mapping in carrot (Daucus carota L.) [abstract]. Plant and Animal Genome Conference. Paper No. P0697.
Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content and rearrangements revealed by next generation sequencing Reprint Icon - (Peer Reviewed Journal)
Fajardo, D., Senalik, D.A., Ames, M., Zhu, H., Steffan, S.A., Harbut, R., Polashock, J.J., Vorsa, N., Gillespie, E., Kron, K., Zalapa, J.E. 2013. Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content and rearrangements revealed by next generation sequencing. Tree Genetics and Genomes. 9(2):489-498.
Rapid reconstruction and annotation of vaccinium macrocarpon organellar genomes - (Abstract Only)
Steffan, S.A., Senalik, D.A., Polashock, J.J., Vorsa, N., Fajardo, D., Harbut, R., Zalapa, J.E. 2012. Rapid reconstruction and annotation of vaccinium macrocarpon organellar genomes [abstract]. Botany 2012 - The Next Generation. Paper. No. 1043.
De novo assembly and characterization of the carrot mitochondrial genome using next generation sequencing data from whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome Reprint Icon - (Peer Reviewed Journal)
Simon, P.W., Iorizzo, M., Senalik, D.A., Szklarczyk, M., Grzebelus, D., Spooner, D.M. 2012. De novo assembly and characterization of the carrot mitochondrial genome using next generation sequencing data from whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome. Biomed Central (BMC) Plant Biology. 12:1-17.
In silico analysis of 454 data yields the complete American cranberry (Vaccinium macrocarpon Ait.) plastid genome - (Abstract Only)
Zalapa, J.E., Steffan, S.A., Simon, P.W., Senalik, D.A., Polashock, J.J., Vorsa, N., Fajardo, D., Harbut, R., Zhu, H., Mccown, B., Zeldin, E. 2012. In silico analysis of 454 data yields the complete American cranberry (Vaccinium macrocarpon Ait.) plastid genome [abstract]. Plant and Animal Genome Conference. Paper No. P0047.
De novo assembly of the carrot mitochondrial genome - (Abstract Only)
Iorizzo, M., Simon, P.W., Senalik, D.A., Szklarczyk, M., Grzeblus, D. 2012. De novo assembly of the carrot mitochondrial genome [abstract]. Plant and Animal Genome Conference. Paper No. P0040.
Progress towards the complete American cranberry (Vaccinium macrocarpon Ait.) plastid genome - (Abstract Only)
Zalapa, J.E., Steffan, S.A., Simon, P.W., Senalik, D.A., Polashock, J.J., Vorsa, N., Diego, F., Harbut, R., Zhu, H. 2011. Progress towards the complete American cranberry (Vaccinium macrocarpon Ait.) plastid genome [abstract]. Plant Sciences Symposium.
Using next generation sequencing approaches for the isolation of simple sequence repeats (SSF) in the plant sciences - (Peer Reviewed Journal)
Zalapa, J.E., Cuevas, H.E., Steffan, S.A., Simon, P.W., Senalik, D.A., Zhu, H., Mccown, B., Zeldin, E., Harbut, R. 2012. Using next generation sequencing approaches for the isolation of simple sequence repeats (SSR) in the plant sciences. American Journal of Botany. 99(2):193-208.
Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.) - (Peer Reviewed Journal)
Zalapa, J.E., Simon, P.W., Hummer, K.E., Bassil, N.V., Senalik, D.A., Zhu, H., Mccown, B.H., Zeldin, E., Speers, J., Hyman, J. 2012. Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.). Theoretical and Applied Genetics. 124(1):87-96.
De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity - (Peer Reviewed Journal)
Iorizzo, M., Senalik, D.A., Grzebelus, D., Bowman, M., Cavagnaro, P.F., Matvienko, M., Ashrafi, H., Van Deynze, A., Simon, P.W. 2011. De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. Biomed Central (BMC) Genomics. 12:389.
Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae - (Peer Reviewed Journal)
Cavagnaro, P.F., Chung, S., Manin, S., Yildiz, M., Ali, A., Alessandro, M.S., Iorizzo, M., Senalik, D.A., Simon, P.W. 2011. Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae. Biomed Central (BMC) Genomics. 12:386.
Comparative FISH mapping of Daucus species (Apiaceae family) - (Peer Reviewed Journal)
Iovene, M., Cavagnaro, P.F., Simon, P.W., Senalik, D.A., Buell, C.R., Jiang, J. 2011. Comparative FISH mapping of Daucus species (Apiaceae family). Chromosome Research. 19:493-506.
The Development of RoBuST: An integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae - (Abstract Only)
Bhasi, A., Simon, P.W., Senalik, D.A., Kumar, B., Manikandan, V., Philge, P., Senapathy, P. 2011. The Development of RoBuST: An integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae [abstract]. Plant and Animal Genome Conference. P. 811.
Development of EST based markers for exploiting the carrot genome - (Abstract Only)
Iorizzo, M., Bowman, M., Simon, P.W., Cavagnaro, P., Senalik, D.A., Carputo, D., Van Deynze, A. 2011. Development of EST based markers for exploiting the carrot genome [abstract]. Plant and Animal Genome Conference. p. 175.
Genome-wide Characterization of Simple Sequence Repeats in Cucumber (Cucumis Sativus L.) - (Peer Reviewed Journal)
Cavagnari, P.F., Weng, Y., Senalik, D.A., Yang, L., Simon, P.W., Harkins, T.T., Kodira, C.D., Huang, S. 2010. Genome-wide Characterization of Simple Sequence Repeats in Cucumber (Cucumis Sativus L.). Biomed Central (BMC) Genomics. Available: http://www.biomedcentral.com/1471-2164/11/569.
Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.) - (Peer Reviewed Journal)
Cavagnaro, P.F., Weng, Y., Senalik, D.A., Simon, P.W., Harkins, T.T., Huang, S. 2010. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). Biomed Central (BMC) Genomics. 11:569-588.
RoBuST: An Integrated Resource of Genomics Information for Plants in the Root and Bulb Crop Families Apiaceae and Alliaceae - (Peer Reviewed Journal)
Bhasi, A., Simon, P.W., Senalik, D.A., Kumar, B., Manikandan, V., Philip, P., Senapathy, P. 2010. RoBuST: An Integrated Resource of Genomics Information for Plants in the Root and Bulb Crop Families Apiaceae and Alliaceae. Biomed Central (BMC) Plant Biology. 10:161.
Genetic Variation Between Two Cucumber Genotypes Inferred from Genome-wide Microsatellite Polymorphism Analysis - (Abstract Only)
Cavagnaro, P., Weng, Y., Senalik, D.A., Harkins, T.T., Kodira, C.D., Simon, P.W., Huang, S. 2010. Genetic Variation Between Two Cucumber Genotypes Inferred from Genome-wide Microsatellite Polymorphism Analysis [abstract]. Plant and Animal Genome Conference. p. 135.
Developing genomic resources for the apiaceae - (Abstract Only)
Bowman, M., Matvienko, M., Van Deynze, A., Simon, P.W., Senalik, D.A. 2010. Developing genomic resources for the apiaceae [abstract]. Plant and Animal Genome Conference. P. 037.
Genome Wide Characterization of Simple Sequence Repeats in Cucumber - (Abstract Only)
Weng, Y., Cavagnaro, P., Senalik, D.A., Harkins, T., Simon, P.W. 2009. Genome Wide Characterization of Simple Sequence Repeats in Cucumber [abstract]. International Symposium on Cucurbits Proceedings. p. 80.
Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences - (Peer Reviewed Journal)
Simon, P.W., Cavagnaro, P.F., Chung, S., Szklarczyk, M., Grzebelus, D., Senalik, D.A., Atkins, A.E. 2009. Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences. Molecular Genetics and Genomics. 281(3):273-288.
SplinkBES - A Splinkerette-Based Method for Generating Long End Sequences From Large Insert DNA Libraries - (Peer Reviewed Journal)
Simon, P.W., Cavagnaro, P.F., Senalik, D.A. 2009. SplinkBES - A Splinkerette-Based Method for Generating Long End Sequences From Large Insert DNA Libraries. Biotechniques. 47:681-690.
Characterization of an Unusual Cytoplasmic Chimera Detected in Bolting Garlic (Allium sativum L.) Clones - (Peer Reviewed Journal)
Ipek, M., Ipek, A., Senalik, D.A., Simon, P.W. 2007. Characterization of an Unusual Cytoplasmic Chimera Detected in Bolting Garlic (Allium sativum L.) Clones. Journal of the American Society for Horticultural Science. 132:664-669.
Path Analysis Suggests Phytoene Accumulation As the Key Step Limiting the Carotenoid Pathway in Roots of White Carrot - (Peer Reviewed Journal)
Santos, C.A., Senalik, D.A., Simon, P.W. 2005. Path analysis suggests phytoene accumulation as the key step limiting the carotenoid pathway in roots of white carrot. Genetics and Molecular Biology. 28:287-293.
Last Modified: 12/19/2014
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