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United States Department of Agriculture

Agricultural Research Service

Related Topics

Douglas Senalik
Vegetable Crops Research
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.)
Fine mapping, transcriptome analysis, and marker development for Y2, the gene that conditions beta-carotene accumulation in carrot (Daucus carota L.) -
Ellison, S., Senalik, D., Bostan, H., Iorizzo, M., Simon, P. 2017. Fine mapping, transcriptome analysis, and marker development for Y2, the gene that conditions beta-carotene accumulation in carrot (Daucus carota L.). G3, Genes/Genomes/Genetics. 7(8)2665-2675. doi: 10.1534/g3.117.043067.
Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae):Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid Reprint Icon -
Spooner, D.M., Ruess, H., Iorizzo, M., Senalik, D., Simon, P. 2017. Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid. American Journal of Botany. 104(2):296-312. doi: 10.3732/ajb.1600415.
Characterization of a genomic region under selection in cultivated carrot (Daucus carota subsp. sativus) reveals a candidate domestication gene Reprint Icon -
Macko-Podgorni, A., Machaj, G., Stelmach, K., Senalik, D., Grzebelus, E., Iorizzo, M., Simon, P.W., Grzebelus, D. 2017. Characterization of a genomic region under selection in cultivated carrot (Daucus carota subsp. sativus) reveals a candidate domestication gene. Frontiers in Plant Science. 8. doi: 10.3389/fpls.2017.00012.
The carrot genome provides insights into crop origins and a foundation for future crop improvement -
Simon, P.W., Iorizzo, M., Ellison, S., Senalik, D.A., Zeng, P., Satapoomin, P., Bowman, M., Iovene, M., Sanseverino, W., Cavagnaro, P., Yildiz, M., Macko-Podgorni, A., Moranska, E., Spooner, D.M. et al. 2016. The carrot genome provides insights into crop origins and a foundation for future crop improvement. Chronica Horticulturae. 56(4):8-13.
Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae) Reprint Icon -
Arbizu, C.I., Ellison, S.L., Senalik, D., Simon, P.W., Spooner, D.M. 2016. Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae). BMC Evolutionary Biology. 16(1):234. doi: 10.1186/s12862-016-0806-x.
A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution Reprint Icon -
Iorizzo, M., Ellison, S., Senalik, D., Zeng, P., Satapoomin, P., Huang, J., Bowman, M., Iovene, M., Sanseverino, W., Cavagnaro, P., Yildiz, M., Spooner, D.M., Simon, P.W., et al. 2016. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nature Genetics. 48(6):657-666. doi: 10.1038/ng.3565.
Genotyping-by-sequencing provides insights into the classification of the subspecies of Daucus carota -
Arbizu, C., Ellison, S., Senalik, D.A., Simon, P.W., Spooner, D.M. 2016. Genotyping-by-sequencing provides insights into the classification of the subspecies of Daucus carota [abstract]. Botany. Paper No. 348.
A complete plastid phylogeny of Daucus – concordance to nuclear results, and markers necessary for phylogenetic resolution -
Spooner, D.M., Ruess, H.M., Senalik, D.A., Simon, P.W. 2016. A complete plastid phylogeny of Daucus – concordance to nuclear results, and markers necessary for phylogenetic resolution [abstract]. Botany. Paper No. 119.
Recent advance in carrot genomics Reprint Icon -
Iorizzo, M., Ellison, S., Van Deynze, A., Stoffel, K., Ashrafi, H., Iovene, M., Cavagnaro, P., Cheng, S., Zheng, P., Zheng, Z., Senalik, D., Spooner, D.M., Simon, P.W. 2017. Recent advance in carrot genomics. Acta Horticulturae. 1153:61-68. doi: 10.17660/ActaHortic.2017.1153.10.
Integrated molecular and morphological studies of Daucus -
Atbizu, C.I., Ruess, H., Senalik, D., Iorizzo, M., Simon, P.W., Spooner, D.M., Reitsma, K. 2017. Integrated molecular and morphological studies of Daucus. Acta Horticulturae. 1153:265-271. doi: 10.17660/ActaHortic.2017.1153.39.
The next generation of carotenoid studies in carrot (Daucus carota L.) -
Ellison, S., Iorrizo, M., Senalik, D., Simon, P.W. 2017. The next generation of carotenoid studies in carrot (Daucus carota L.). Acta Horticulturae. 1153:93-100. doi: 10.17660/ActaHortic.2017.1153.14.
A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation Reprint Icon -
Cavagnaro, P.F., Iorizzo, M., Yildiz, M., Senalik, D.A., Parsons, J., Ellison, S., Simon, P.W. 2014. A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation. Biomed Central (BMC) Genomics. 15:1118.
Integrated molecular and morphological studies of Daucus -
Arbizu, C., Ruess, H., Senalik, D., Simon, P., Reitsma, K., Spooner, D. 2015. Integrated molecular and morphological studies of Daucus [abstract]. Plant and Animal Genome Conference. Paper No. P1074.
Phylogenomics of the carrot genus (Daucus, Apiaceae) Reprint Icon -
Arbizu, C., Ruess, H., Senalik, D., 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 -
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 -
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 -
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 -
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 -
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 -
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) -
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 -
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 -
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 -
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.) -
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.) -
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.) -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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.) -
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 -
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 -
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) -
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 -
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 -
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.) -
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.
Genome-wide Characterization of Simple Sequence Repeats in Cucumber (Cucumis Sativus L.) -
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.
RoBuST: An Integrated Resource of Genomics Information for Plants in the Root and Bulb Crop Families Apiaceae and Alliaceae -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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: 08/23/2017
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