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United States Department of Agriculture

Agricultural Research Service

Juan Zalapa
Research Geneticist


Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Nonstructural carbohydrates and return bloom potential differ among cranberry cultivars -
Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping Reprint Icon -
Covarrubias-Pazaran, G., Diaz-Garcia, L., Schlautman, B., Deutsch, J., Salazar, W., Hernandez-Ochoa, M., Grygleski, E., Steffan, S., Iorizzo, M., Polashock, J.J., Vorsa, N., Zalapa, J. 2016. Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping. Biomed Central (BMC) Genomics. 17(1):451. doi: 10.1186/s12864-016-2802-3.
Fragman: an R package for fragment analysis Reprint Icon -
Covarrubias-Pazaran, G., Diaz-Garcia, L., Schlautman, B., Salazar, W., Zalapa, J. 2016. Fragman: an R package for fragment analysis. BioMed Central (BMC) Genetics. 17(1):62. doi: 10.1186/s12863-016-0365-6.
Conservation of genetic diversity in slippery elm (Ulmus rubra) in Wisconsin despite the devastating impact of Dutch elm disease Reprint Icon -
Brunet, J., Zalapa, J., Guries, R. 2016. Conservation of genetic diversity in slippery elm (Ulmus rubra) in Wisconsin despite the devastating impact of Dutch elm disease. Conservation Genetics. 17(5):1001-1010. doi: 10.1007/s10592-016-0838-1.
Discriminating power of microsatellites in cranberry organelles for taxonomic studies in Vaccinium and Ericaceae -
Schlautman, B., Covarrubias-Pazaran, G., Fajardo, D., Steffan, S., Zalapa, J. 2016. Discriminating power of microsatellites in cranberry organelles for taxonomic studies in Vaccinium and Ericaceae. Genetic Resources and Crop Evolution. doi: 10.1007/s10722-016-0371-6.
Are we on the right track: Can our understanding of abscission in model systems promote or derail making improvements in less studied crops Reprint Icon -
Patterson, S.E., Bolivar-Medina, J.L., Falbel, T.G., Hedtcke, J.L., Nevarez-McBride, D., Maule, A.F., Zalapa, J.E. 2016. Are we on the right track: Can our understanding of abscission in model systems promote or derail making improvements in less studied crops? Frontiers in Plant Science. 6(1268). doi: 10.3389/fpls.2015.01268.
Microbes are trophic analogs of animals Reprint Icon -
Steffan, S.A., Chikaraishi, Y., Currie, C.R., Horn, H., Gaines Day, H.R., Pauli, J.N., Zalapa, J.E., Ohkouchi, N. 2015. Microbes are trophic analogs of animals. Proceedings of the National Academy of Sciences. 112(49):15119-15124. doi: 10.1073/pnas.1508782112.
Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection Reprint Icon -
Schlautman, B., Covarrubias-Pazaran, G., Diaz-Garcia, L.A., Johnson-Cicalese, J., Iorrizo, M., Rodriguez-Bonilla, L., Bougie, T., Bougie, T., Wiesman, E., Steffan, S., Polashock, J., Vorsa, N., Zalapa, J. 2015. Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection. Molecular Breeding. 35(8):177. doi: 10.1007/s11032-015-0367-5.
Beneficial or not? Decoding carnivore roles in plant protection Reprint Icon -
Steffan, S.A., Chikaraishi, Y., Horton, D.R., Miliczky, E., Zalapa, J.E., Jones, V.P., Ohkouchi, N. 2015. Beneficial or not? Decoding carnivore roles in plant protection. Biological Control. 91:34-41. doi: 10.1016/j.biocontrol.2015.07.002.
Switchgrass (Panicum virgatum L.) genotypes differ between coastal sites and inland road corridors in the Northeastern US Reprint Icon -
Ecker, G., Zalapa, J., Auer, C. 2015. Switchgrass (Panicum virgatum L.) genotypes differ between coastal sites and inland road corridors in the Northeastern US. PLoS One. 10(6). doi: 10.1371/journal.pone.0130414.
Evaluating the relationship between diploid and tetraploid Vaccinium oxycoccos (Ericaceae) in eastern Canada Reprint Icon -
Smith, T.W., Walinga, C., Wang, S., Kron, P., Suda, J., Zalapa, J. 2015. Evaluating the relationship between diploid and tetraploid Vaccinium oxycoccos (Ericaceae) in eastern Canada. Botany. 93(10):623-636. doi: 10.1139/cjb-2014-0223.
Yield estimation in commercial cranberry systems using physiological, environmental, and genetic variables Reprint Icon -
DeVetter, L., Colquhoun, J., Zalapa, J., Harbut, R. 2015. Yield estimation in commercial cranberry systems using physiological, environmental, and genetic variables. Scientia Horticulturae. 190(1):83-93.
Toxicity of chelated iron (Fe-DTPA) in American cranberry Reprint Icon -
Siebach, S., Zalapa, J., Covarrubias-Pazaran, G., Harbut, R., Workmaster, B., Wasko DeVetter, L., Steffan, S., Guedot, C., Atucha, A. 2015. Toxicity of chelated iron (Fe-DTPA) in American cranberry. Journal of Horticulture. 2:129. DOI:10.4172/2376-0354.1000128.
Development and validation of 697 novel polymorphic genomic and EST-SSR Markers in the American cranberry (Vaccinium macrocarpon Ait.) Reprint Icon -
Schlautman, B., Fajardo, D., Bougie, T., Wiesman, E., Polashock, J., Vorsa, N., Steffan, S., Zalapa, J. 2015. Development and validation of 697 novel polymorphic genomic and EST-SSR Markers in the American cranberry (Vaccinium macrocarpon Ait.). Molecules. 20(2):2001-2013.
Temperature-mediated development thresholds of Sparganothis sulfureana (Lepidoptera: Tortricidae) in cranberries Reprint Icon -
Deutsch, A.E., Rodriguez-Saona, C.R., Zalapa, J.E., Steffan, S.A. 2015. Temperature-mediated development thresholds of Sparganothis sulfureana (Lepidoptera: Tortricidae) in cranberries. Environmental Entomology. 44(2):400-405.
Clonal diversity and genetic differentiation revealed by SSR markers in wild Vaccinium macrocarpon and Vaccinium oxycoccos Reprint Icon -
Zalapa, J.E., Bougie, T.C., Bougie, T.A., Schlautman, B.J., Wiesman, E., Guzman, A., Fajardo, D.A., Steffan, S., Smith, T. 2014. Clonal diversity and genetic differentiation revealed by SSR markers in wild Vaccinium macrocarpon and Vaccinium oxycoccos. Annals of Applied Biology. 166(2):196-207.
Degree-day benchmarks for Sparganothis sulfureana (Lepidoptera: Tortricidae) development in cranberries Reprint Icon -
Deutsch, A.E., Rodriguez-Saona, C.R, Kyryczenko-Roth, V., Sojka, J., Zalapa, J.E., Steffan, S.A. 2014. Degree-day benchmarks for Sparganothis sulfureana (Lepidoptera: Tortricidae) development in cranberries. Journal of Economic Entomology. 107(6):2130-2136.
A phenology model for Sparganothis fruitworm in Cranberries -
Steffan, S.A., Deutsch, A., Rodriguez-Saona, C., Zalapa, J.E., Kyryczenko-Roth, V. 2014. A phenology model for Sparganothis fruitworm in Cranberries. American Cranberry Growers Association.
Strong evidence of mating disruption despite heavy fruitworm pressure -
Steffan, S.A., Chasen, E.M., Zalapa, J.E. 2014. Strong evidence of mating disruption despite heavy fruitworm pressure. Cranberry Crop Management Newsletter. XXVII(6):4-8.
The American cranberry crowned jewel of the bog at the 2014 U.S.A. Science & Engineering Festival -
Zalapa, J.E., Wiesman, E.C., Schlautman, B., Covarrubias, E. 2014. The American cranberry crowned jewel of the bog at the 2014 U.S.A. Science & Engineering Festival. Wisconsin State Cranberry Growers Association. XXV(7):18.
When and how long to flood for insect control -
Steffan, S.A., Singleton, M., Zalapa, J.E. 2014. When and how long to flood for insect control. Cranberry Crop Management Newsletter. XXVII(3):1-5.
The American cranberry: first insights into the whole genome of a species adapted to bog habitat Reprint Icon -
Polashock, J.J., Zelzion, U., Fajardo, D.A., Zalapa, J.E., Georgi, L., Bhattacharya, D., Vorsa, N. 2014. The American cranberry: first insights into the whole genome of a species adapted to bog habitat. Biomed Central (BMC) Plant Biology. 14:165.
Beneficial or not? Carnivore trophic position under the lens of amino acid isotopic analysis -
Steffan, S.A., Chikaraishi, Y., Horton, D.R., Miliczky, E., Zalapa, J.E., Jones, V., Ohkouchi, N. 2014. Beneficial or not? Carnivore trophic position under the lens of amino acid isotopic analysis [abstract]. Entomological Society of America Annual Meeting. Paper No. 1420.
The use of sequence-based SSR mining for the development of a vast collection of microsatellites in Aquilegia formosa Reprint Icon -
Schlautman, B., Pfeiffer, V., Zalapa, J., Brunet, J. 2014. The use of sequence-based SSR mining for the development of a vast collection of microsatellites in Aquilegia formosa. American Journal of Plant Sciences. 5(15):2402-2412.
Trophic spectra under the lens of amino acid isotopic analysis -
Steffan, S.A., Chikaraishi, Y., Horton, D.R., Miliczky, E., Zalapa, J.E., Jones, V., Ohkouchi, N. 2014. Trophic spectra under the lens of amino acid isotopic analysis [abstract]. Entomological Society of America Annual Meeting North Central Branch.
Generation and characterization of a sugarbeet transcriptome and transcript-based SSR markers -
Fugate, K.K., Fajardo, D., Schlautman, B., Ferrareze, J.P., Bolton, M.D., Campbell, L.G., Wiesman, E.C., Zalapa, J.E. 2014. Generation and characterization of a sugarbeet transcriptome and transcript-based SSR markers. The Plant Genome. 7(2) doi: 10.3835/plantgenome2013.11.0038.
Pheromone-based mating disruption in Wisconsin cranberries -
Deutsch, A., Mafra-Neto, A., Sojka, J., Dittl, T., Zalapa, J.E., Steffan, S.A. 2014. Pheromone-based mating disruption in Wisconsin cranberries [abstract]. Wisconsin State Cranberry Growers Association.
The American cranberry mitochondrial genome reveals the presence of selenocysteine (tRNA-Sec and SECIS) insertion machinery in land plants Reprint Icon -
Fajardo, D., Schlautman, B., Steffan, S.A., Polashock, J.J., Vorsa, N., Zalapa, J.E. 2014. The American cranberry mitochondrial genome reveals the presence of selenocysteine (tRNA-Sec and SECIS) insertion machinery in land plants. Gene. 536(2):336-343.
Multi-species mating disruption in Wisconsin cranberries -
Deutsch, A., Sojka, J., Dittl, T., Mafra-Neto, A., Zalapa, J.E., Steffan, S.A. 2013. Multi-species mating disruption in Wisconsin cranberries [abstract]. National Meeting of Entomological Society Of America. Paper No. 0711.
Stage-specific development of Sparganothis sulfureana (Lepidoptera: Tortricidae) -
Deutsch, A., Kyryczenko-Roth, V., Rodriguez-Saona, C., Zalapa, J.E., Steffan, S.A. 2013. Stage-specific development of Sparganothis sulfureana (Lepidoptera: Tortricidae) [abstract]. North American Cranberry Research and Extension Workers Annual Meeting. p. 1.
Multi-species mating disruption in cranberries -
Deutsch, A., Sojka, J., Dittl, T., Mafra-Neto, A., Zalapa, J.E., Steffan, S.A. 2013. Multi-species mating disruption in cranberries [abstract]. North American Cranberry Research and Extension Workers Annual Meeting. p. 2.
Sparganothis fruitworm biology and phenology -
Steffan, S.A., Deutsch, A., Kyryczenko-Roth, V., Rodriguez-Saona, C., Zalapa, J.E. 2013. Sparganothis fruitworm biology and phenology [abstract]. North American Cranberry Research and Extension Workers Annual Meeting. p. 2.
Hybridization and introgression between the exotic Siberian elm, Ulmus pumila, and the native Field elm, U. minor, in Italy Reprint Icon -
Brunet, J., Zalapa, J.E., Pecori, F., Santini, A. 2013. Hybridization and introgression between the exotic Siberian elm, Ulmus pumila, and the native Field elm, U. minor, in Italy. Biological Invasions. Available: http://link.springer.com/article/10.1007%2Fs10530-013-0486-z.
Systematic and functional implications of structural rearrangements in whole chloroplast genomes of Ericaceae -
Zalapa, J.E., Kron, K., Gillespie, E., Fajardo, D. 2013. Systematic and functional implications of structural rearrangements in whole chloroplast genomes of Ericaceae [abstract]. Association of Southeastern Biologists. Paper No. 117.
Spotted Wing Drosophila, Sparganothis phenology and a new look at the BugFloods -
Steffan, S.A., Lee, J.C., Deutsch, A., Singleton, M., Rodriguez-Saona, C., Zalapa, J.E. 2013. Spotted Wing Drosophila, Sparganothis phenology and a new look at the BugFloods. Wisconsin Cranberry School. 21:1-6.
Cranberries and Spotted Wing Drosophila (SWD) in Wisconsin -
Steffan, S.A., Lee, J.C., Lavine, L., Walsh, D., Metzger, C., Zalapa, J.E., Guedot, C., Pellitteri, P. 2012. Cranberries and Spotted Wing Drosophila (SWD) in Wisconsin. Wisconsin State Cranberry Growers Association. XXIII(11):13.
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.
Flooding as “spring cleaning” for insect pests -
Steffan, S.A., Singleton, M., Sojka, J., Zalapa, J.E., Dittl, T. 2012. Flooding as “spring cleaning” for insect pests. Wisconsin State Cranberry Growers Association. p. 32-34.
Removal of arthropods in the spring “trash floods” -
Steffan, S.A., Singleton, M., Sojka, J., Zalapa, J.E. 2012. Removal of arthropods in the spring “trash floods”. Wisconsin State Cranberry Growers Association. XXV(7):3-4.
The record-breaking 2012 spring: Why degree-days were critical in assessing insect and plant development -
Steffan, S.A., Singleton, M., Deutsch, A., Bosak, L., Zalapa, J.E. 2012. The record-breaking 2012 spring: Why degree-days were critical in assessing insect and plant development. Wisconsin State Cranberry Growers Association. p. 29-31.
The warm winter and spring of 2012: Why degree-days were critical in measuring insect and plant development -
Steffan, S.A., Singleton, M., Deutsch, A., Bosak, L., Zalapa, J.E. 2012. The warm winter and spring of 2012: Why degree-days were critical in measuring insect and plant development. Wisconsin State Cranberry Growers Association. XXV(7):1-2.
Discrimination of American cranberry cultivars and assessment of clonal heterogeneity using microsatellite markers -
Fajardo, D., Morales, J., Zhu, H., Steffan, S.A., Harbut, R., Bassil, N.V., Hummer, K.E., Polashock, J.J., Vorsa, N., Zalapa, J.E. 2012. Discrimination of American cranberry cultivars and assessment of clonal heterogeneity using microsatellite markers. Plant Molecular Biology Reporter. 31(2):264-271.
Bottle biology: Making cranberry cutting tubbe necklaces -
Zalapa, J.E., Gustin, E.S., Steffan, S.A., Harbut, R., Bryan, T., Fajardo, D., Williams, P., Trumble, H. 2012. Bottle biology: Making cranberry cutting tubbe necklaces [abstract]. Botany 2012 - The Next Generation. Paper No. 1059.
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.
Early-season flooding for insect pest control -
Steffan, S.A., Singleton, M., Sojka, J., Zalapa, J.E., Harbut, R. 2012. Early-season flooding for insect pest control. Wisconsin Cranberry School 2012 Proceedings. 20:24-28.
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.
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.
A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.) -
Diaz, A., Fergany, M., Formisano, G., Ziarsolo, P., Blanca, J., Staub, J.E., Cuevas, H.E., Zalapa, J.E. 2011. A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.). BMC Microbiology. www.biomedcwntral.com/1471-2229/11/111.
Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping -
Li, D., Weng, Y., Cuevas, H., Yang, L., Li, Y., Garcia-Mas, J., Zalapa, J.E., Staub, J.E., Luan, F., Reddy, U., He, X., Gong, Z. 2011. Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping. Biomed Central (BMC) Genomics. 12:396-409.
Development of educational tools to connect public audiences with cranberry researchers and growers -
Zalapa, J.E., Steffan, S.A., Harbut, R., Fredette, N. 2011. Development of educational tools to connect public audiences with cranberry researchers and growers [abstract]. North American Cranberry Research and Extension Workers Annual Meeting. Paper No. 8.
Measuring genetic diversity and purity of cranberry clonal cultivars using microsatellite markers -
Zalapa, J.E., Steffan, S.A., Hummer, K.E., Bassil, N.V., Moreno, J., Zhu, H., Mccown, B., Zeldin, E., Harbut, R. 2011. Measuring genetic diversity and purity of cranberry clonal cultivars using microsatellite markers [abstract]. North American Cranberry Research and Extension Workers Annual Meeting. Paper No. 5.
Re-visiting spring flooding as an IPM approach in Wisconsin cranberries -
Steffan, S.A., Zalapa, J.E., Singleton, M., Harbut, R. 2011. Re-visiting spring flooding as an IPM approach in Wisconsin cranberries [abstract]. North American Cranberry Research and Extension Workers Annual Meeting. p. 18.
Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences Reprint Icon -
Zhang, Y., Zalapa, J.E., Jakubowski, A.R., Price, D.L., Acharya, A., Wei, Y., Brummer, E.C., Kaeppler, S.M., Casler, M.D. 2011. Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences. Genetica. 139:933-948.
Natural hybrids and gene flow between upland and lowland switchgrass Reprint Icon -
Zhang, Y., Zalapa, J.E., Jakubowski, A.R., Price, D.L., Acharya, A., Wei, Y., Brummer, E.C., Kaeppler, S.M., Casler, M.D. 2011. Natural hybrids and gene flow between upland and lowland switchgrass. Crop Science. 51:2626-2641.
USDA 846-1 fractal melon and derived recombinant inbred lines -
Staub, J.E., Mccreight, J.D., Zalapa, J.E. 2011. USDA 846-1 fractal melon and derived recombinant inbred lines. HortScience. 46:1423-1425.
Last Modified: 8/26/2016
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