Research Leader
https://orcid.org/0000-0001-6464-2529
Educational Background
1995-2000 University of Khartoum; major, Horticulture; B.S. 2000.
2004-2006 South Dakota State University; major, Plant Science; minor, plant breeding and genetics; M.Sc. 2006.
2007-2012 Washington State University; major, Plant Pathology; minor, plant breeding and genetics; Ph.D. 2012.
Professional Experience:
2004-2007, Graduate Research Assistant, South Dakota State University, Brookings, SD.
2007-2012, Graduate Research Assistant, Washington State University, Pullman, WA.
2012-2016, Research Plant Pathologist, USDA-ARS NSGC, Aberdeen, ID.
2016-2024, Research Plant Geneticist, USDA-ARS TCSHL, Poplarville, MS.
March 2024-present, Supervisory Research Geneticist and Research Leader of the USDA ARS Corn Host Resistance Research Unit, Mississippi State, MS.
Research Specialty and Interests:
The long-term objective of the research project is to identify and develop corn germplasm with genetic resistance to Aspergillus flavus infection and the subsequent accumulation of aflatoxin and genetic resistance to insect damage using both conventional breeding methods and marker assisted selection. In support of this objective, I work with interdisciplinary research team in cooperation with scientists in ARS and other institutions to (1) identify new corn germplasm sources with resistance to A. flavus infection and aflatoxin accumulation; (2) identify genes and elucidate functions of genes associated with resistance to aflatoxin accumulation, and develop molecular markers for enhancing maize germplasm with resistance; (3) develop and release maize germplasm lines with resistance to aflatoxin accumulation or damage by southwestern corn borer and fall armyworm; and (4) evaluate the effectiveness of genetic resistance to aflatoxin accumulation when deployed with other control strategies.
Projects
Genetic Improvement of Maize for Resistance to Aflatoxin Accumulation and Fall Armyworm Damage In-House Appropriated (D) Accession Number:445200 
Expanding Southern Highbush Blueberries To Underserved Regions of Southeastern U.S. Reimbursable Cooperative Agreement (R) Accession Number:445438 Establishing CRISPR/Cas9-mediated Targeted Mutagenesis Protocol to Develop Seedless Muscadine Grape Non-Assistance Cooperative Agreement (S) Accession Number:440391 Screening Muscadine Grape for Resistance to Pierce’s Disease Pathogen Non-Assistance Cooperative Agreement (S) Accession Number:443317
Publications
will take you to the publication reprint.)
-(Peer Reviewed Journal)
Hilsop, L.M., Luby, C.H., Loarca, J., Humann, J., Hummer, K.E., Bassil, N.V., Zhao, D., Sheehan, M., Casa, A.M., Billings, G.T., Echeverria, D., Ashrafi, H., Babiker, E.M., Edger, P., Ehlenfeldt, M.K., Hancock, J., Finn, C.E., Iorizzo, M., Mackey, T.A., Munoz, P.R., Olmstead, J., Rowland, L.J., Sandefur, P., Spencer, J., Stringer, S.J., Vorsa, N., Wagner, A., Hulse-Kemp, A.M. 2024. A blueberry (Vaccinium spp.) crop ontology to enable standardized phenotyping for blueberry breeding and research. Journal of the American Pomological Society. 59:1433-1442. https://doi.org/10.21273/HORTSCI17676-23. -(Peer Reviewed Journal)
Clare, S.J., Driskill, M., Millar, T.R., Chagne, D., Montanari, S., Thomson, S., Espley, R.V., Munoz, P., Benevenuto, J., Zhao, D., Sheehan, M., Mengist, M.F., Rowland, L.J., Ashrafi, H., Melmaiee, K., Kulkarni, K.P., Babiker, E.M., Main, D., Olmstead, J.W., Gilbert, J.L., Havlak, P., Hung, H., Kniskern, J., Percival, D., Edger, P., Iorizzo, M., Bassil, N.V. 2024. Development of a targeted genotyping platform for reproducible results within tetraploid and hexaploid blueberry. Frontiers in Horticulture. 2. Article 1339310. https://doi.org/10.3389/fhort.2023.1339310. -(Peer Reviewed Journal)
Dobbs, J.T., Caballero, J.R., Ata, J.P., Babiker, E.M., Copes, W.E., Stewart, J.E. 2024. Genomic and transcriptomic comparisons of the twig blight pathogen, Passalora sequoiae with Mycosphaereallaceae foliar and conifer pathogens. Phytopathology. 114:732-742. https://doi.org/10.1094/PHYTO-08-23-0271-R.
Bassil, N.V., Hislop, L., Hulse-Kemp, A.M., Zhang, D., Sheehan, M., Humann, J., Main, D., Iorizzo, M., Babiker, E.M. 2024. Developing a new crop ontology for blueberry. Plant and Animal Genome Conference. -(Peer Reviewed Journal)
Huff, M., Babiker, E.M., Hulse-Kemp, A.M., Scheffler, B.E., Youngblood, R.C., Simpson, S.A., Staton, M. 2023. Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa. BMC Genomics. https://doi.org/10.1186/s12864-023-09514-y. -(Peer Reviewed Journal)
Babiker, E.M., Stringer, S.J., Sakhanokho, H.F., Munoz, P. 2023. Combining high throughput phenotyping and multivariate analysis to assess fruit quality traits in southern highbush blueberry (V. corymbosum interspecific hybrids) germplasm collection. HortScience. 58(7):750-755. https://doi.org/10.21273/HORTSCI17185-23.
Bassil, N.V., Clare, S.J., Driskill, M., Zheng, P., Chagne, D., Montanari, S., Thompson, S., Espley, R., Munoz, P., Benevenuto, J., Zhao, D., Sheehan, M., Mengist, M., Rowland, L.J., Ashrafi, H., Melmaiee, K., Babiker, E.M., Olmstead, J., Gilbert, J., Kniskern, J., Main, D., Zalapa, J.E., Polashock, J.J., Edger, P., Iorizzo, M. 2023. VacCAP develops high throughput genotyping platforms for blueberry and cranberry. HortScience. -(Peer Reviewed Journal)
Stringer, S.J., Draper, A.D., Babiker, E.M., Sampson, B.J., Sakhanokho, H.F. 2023. 'USDA-Spiers' rabbiteye blueberry. HortScience. 58(3):338–340. https://doi.org/10.21273/HORTSCI17042-22. -(Peer Reviewed Journal)
Sampson, B., Stringer, S., Hummer, K., Babiker, E., Werle, C., Adamczyk, J. and Shaw, D., 2023. Evaluating global Vaccinium germplasm for resistance against invasive Drosophila suzukii (Diptera: Drosophilidae). Journal of Economic Entomology, p.toad081. https://doi.org/10.1093/jee/toad081 -(Peer Reviewed Journal)
Bowden, A.T., Knight, P.R., Ryals, J.B., Coker, C.E., Langlois, S.A., Broderick, S.R., Blythe, E.K., Sakhanokho, H.F., Babiker, E.M. 2022. Evaluation of one-time applications of foliar applied auxin co-applied with surfactant for use in commercial cutting propagation. Agronomy Journal. 12(10):2243. https://doi.org/10.3390/agronomy12102243.
Werle, C.T., Babiker, E.M., Adamczyk Jr, J.J. 2022. Seasonal abundance and diversity of potential Xylella (Xanthomonadales: xanthomonadaceae) vectoring leafhoppers in Mississippi muscadine vineyards. Subtropical Agriculture and Environments. 73:1-8.
Werle, C.T., Babiker, E.M., Adamczyk Jr, J.J. 2022. Seasonal abundance and diversity of potential Xylella (Xanthomonadales: xanthomonadaceae) vectoring leafhoppers in Mississippi muscadine vineyards. Subtropical Agriculture and Environments. 73:1-8. -(Peer Reviewed Journal)
Edger, P.P., Iorizzo, M., Bassil, N.V., Benevenuto, J., Ferrao, L.F., Giongo, L., Hummer, K.E., Lawas, L.F., Leisner, C.P., Li, C., Munoz, P., Ashrafi, H., Atucha, A., Babiker, E.M., Canales, E., Chagne, D., DeVetter, L., Ehlenfeldt, M.K., Espley, R.V., Gallardo, K., Gunther, C.S., Hardigan, M.A., Hulse-Kemp, A.M., Jacobs, M.L., Lila, M., Luby, C.H., Main, D., Mengist, M.F., Owens, G.L., Perkins-Veazie, P., Polashock, J.J., Pottorff, M., Rowland, L.J., Sims, C.A., Song, G., Spencer, J., Vorsa, N., Yocca, A.E., Zalapa, J.E. 2022. There and back again; historical perspective and future directions for Vaccinium breeding and research studies. Horticulture Research. 9. Article uhac083. https://doi.org/10.1093/hr/uhac083.
Bassil, N.V., Driskill, M., Edger, P., Chagne, D., Montanari, S., Thompson, S., Espley, R., Munoz, P., Benevenuto, J., Zhao, D., Sheehan, M., Fentie, M., Rowland, L.J., Ashrafi, H., Melmaiee, K., Babiker, E.M., Olmstead, J., Gilbert, J., Kniskern, J., Wells, M., Iorizzo, M. 2022. VacCAP produces a targeted capture genotyping platform for blueberry. Acta Horticulturae. -(Peer Reviewed Journal)
Nagasaka, K., Nishiyama, S., Fujikawa, M., Yamane, H., Shirasawa, K., Babiker, E.M., Tao, R. 2022. Genome-wide identification of loci associated with phenology-related traits and their adaptive variations in a highbush blueberry collection. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2021.793679. -(Peer Reviewed Journal)
Yu, J., Hulse-Kemp, A.M., Babiker, E.M., Staton, M. 2021. High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii). Horticulture Research. 8:228. https://doi.org/10.1038/s41438-021-00641-9. -(Peer Reviewed Journal)
Gordon, T.C., Jin, Y., Gale, S.W., Rouse, M.N., Stoxen, S.M., Wanyera, R., Macharia, G., Randhawa, M., Bhavani, S., Brown Guedira, G.L., Marshall, D.S., Babiker, E.M., Bockelman, H.E., Bonman, J.M. 2021. Identification of winter habit bread wheat landraces in the national small grains collection with resistance to emerging stem rust pathogen variants. Plant Disease. 105(12):3998-4005. https://doi.org/10.1094/PDIS-04-21-0743-RE. -(Peer Reviewed Journal)
Sakhanokho, H.F., Islam-Faridi, N., Babiker, E.M., Smith, B.J. 2021. Micropropagation of Hibiscus moscheutos L. ‘Luna White’: Effect of growth regulators and explants on nuclear DNA content and ploidy stability of regenerants. In Vitro Cellular and Developmental Biology - Plants. doi.org/10.1007/s11627-021-10209-w. -(Peer Reviewed Journal)
Copes, W.E., Ibarra Caballero, J., Babiker, E.M., Stewart, J.E., Orner, V.A., Windham, A.S., Arias De Ares, R.S. 2020. Draft genome assembly of Passalora sequoiae a needle blight pathogen on leyland cypress. BMC Research Notes. 13:505. https://doi.org/10.1186/s13104-020-05328-3. -(Peer Reviewed Journal)
Nishiyama, S., Fujikawa, M., Yamane, H., Shirasawa, K., Babiker, E.M., Tao, R. 2020. Genomic insight into the developmental history of southern highbush blueberry populations. Heredity. https://doi.org/10.1038/s41437-020-00362-0. -(Peer Reviewed Journal)
Mavrodi, O.V., Mavrodi, D.V., Stafine, E.T., Adamczyk Jr, J.J., Babiker, E.M. 2020. Draft genome sequences of Xylella fastidiosa subsp. fastidiosa strains OK3, VB11, and NOB1 isolated from bunch and muscadine grapes grown in southern Mississippi. Microbiology Resource Announcements. 9(25):1-2. https://doi.org/10.1128/MRA.00562-20. -(Peer Reviewed Journal)
Li, J., Mavrodi, O., Hou, J., Blackman, C., Babiker, E.M., Mavrodi, D. 2020. Comparative analysis of rhizosphere microbiomes of southern highbush blueberry (Vaccinium corymbosum L.), Darrow’s blueberry (V. darrowii Camp.), and rabbiteye blueberry (V. virgatum Aiton). Frontiers in Microbiology. 11:370. https://www.frontiersin.org/articles/10.3389/fmicb.2020.00370/full. -(Peer Reviewed Journal)
Sakhanokho, H.F., Islam-Faridi, N., Babiker, E.M., Nelson, C., Stringer, S.J., Adamczyk Jr, J.J. 2020. Determination of nuclear DNA content, ploidy, and FISH location of ribosomal DNA in Hibiscus hamabo. Scientia Horticulturae. 264:109167. https://doi.org/10.1016/j.scienta.2019.109167. -(Peer Reviewed Journal)
Kebede, A.Z., Yimer, B.A., Bekele, W., Gordon, T.C., Bonman, J.M., Babiker, E.M., Jin, Y., Gale, S.W., Wight, C.P., Tinker, N., Menzies, J., Beattie, A., Mitchell-Fetch, J., Fetch, T., Esvelt Klos, K.L., McCartney, C. 2019. Mapping of the stem rust resistance gene Pg13 in cultivated oat. Journal of Theoretical and Applied Genetics. 133:259-270. https://doi.org/10.1007/s00122-019-03455-5. -(Peer Reviewed Journal)
Babiker, E.M., Stringer, S.J., Sakhanokho, H.F., Smith, B.J., Polashock, J.J. 2019. Characterization and pathogenicity of stem blight complex isolates associated with stem blight disease on Vaccinium species. HortScience. 54:1199-1203. https://doi.org/10.21273/HORTSCI14033-19.
Sakhanokho, H.F., Babiker, E.M., Smith, B.J., Drackett, P.R. 2019. High-frequency somatic embryogenesis, nuclear DNA estimation, and genome size stability of micropropagated milkweed (Asclepias spp.) plants. Plant Cell Tissue and Organ Culture. 137:149-156. -(Peer Reviewed Journal)
Babiker, E.M., Stringer, S.J., Adamczyk Jr, J.J., Sakhanokho, H.F., Draper, A. 2018. ‘Muffin Man’ an edible ornamental rabbiteye blueberry. HortScience. 53(10):1523-1524. https://doi.org/10.21273/HORTSCI13372-18. -(Peer Reviewed Journal)
Babiker, E.M., Stringer, S.J., Smith, B.J., Sakhanokho, H.F. 2018. Reaction of different vaccinium species to the blueberry leaf rust pathogen Thekopsora minima. HortScience. 53(10):1447-1452. https://doi.org/10.21273/HORTSCI13319-18. -(Peer Reviewed Journal)
Gallardo, R.K., Zhang, Q., Klingthong, P., Dossett, M., Polashock, J.J., Rodriguez-Saona, C., Vorsa, N., Edger, P., Scherm, H., Ashrafi, H., Babiker, E.M., Finn, C.E., Iorizzo, M. 2018. Breeding trait priorities of the blueberry industry in the United States and Canada. HortScience. 53(7):1021-1028. https://doi.org/10.21273/HORTSCI12964-18. -(Peer Reviewed Journal)
Miller Butler, M.A., Smith, B.J., Babiker, E.M., Kreiser, B.R., Blythe, E.K. 2018. Comparison of whole plant and detached leaf screening techniques for identifying anthracnose resistance in strawberry plants. Plant Disease. 102(11):2112-2119. https://doi.org/10.1094/PDIS-08-17-1138-RE. -(Peer Reviewed Journal)
Gao, L., Babiker, E.M., Nava, I.C., Nirmala, J., Bedo, Z., Lang, L., Chao, S., Gale, S.W., Jin, Y., Anderson, J.A., Bansal, U., Park, R.F., Rouse, M.N., Bonman, J.M., Bariana, H. 2018. Temperature-sensitive wheat stem rust resistance gene Sr15 is effective against Puccinia graminis f. sp. tritici race TTKSK. Plant Pathology. http://doi.org/10.1111/ppa.12928. -(Peer Reviewed Journal)
Mahoney, A., Babiker, E.M., Okubara, P.A., See, D.R., Paulitz, T.C., Hulbert, S.H. 2017. Analysis and mapping of Rhizoctonia root rot resistance traits from the synthetic wheat (Triticum aestivum L.) line SYN-172. Molecular Breeding. 37:130. https://doi.org/10.1007/s11032-017-0730-9.
Kankwatsa, P., Singh, D., Thomson, P., Newcomb, M., Babiker, E.M., Bonman, J.M., Park, R.F. 2017. Characterization and genome-wide association mapping of resistance to leaf rust, stem rust and stripe rust in a geographically diverse collection of spring wheat landraces. Molecular Breeding. 37(9):1-24. doi:10.1007/s1103201707078.
Esvelt Klos, K.L., Yimer, B.A., Babiker, E.M., Beattie, A.D., Bonman, J.M., Carson, M.L., Chong, J., Harrison, S.A., Ibrahim, A.H., Kolb, F.L., McCartney, C.A., McMullen, M., Mitchell Fetch, J., Mohammadi, M., Murphy, J.P., Tinker, N.A. 2017. Genome-wide association mapping of crown rust resistance in oat elite germplasm. The Plant Genome. doi: 10.3835/plantgenome2016.10.0107.
Babiker, E.M., Gordon, T.C., Chao, S., Rouse, M.N., Jin, Y., Bhavani, S., Wanyera, R., Newcomb, M., Bonman, J.M. 2017. Genetic loci conditioning adult plant resistance to the Ug99 race group and seedling resistance to races TRTTF and TTTTF of the stem rust pathogen in wheat landrace CItr 15026. Plant Disease. 101(3):496-501.
Babiker, E.M., Gordon, T.C., Chao, S., Rouse, M.N., Acevedo, M., Wanyera, R., Brown Guedira, G.L., Bonman, J.M. 2017. Molecular mapping of stem rust resistance loci effective against the Ug99 race group of the stem rust pathogen and identification of SNP marker linked to stem rust resistance gene Sr28. Phytopathology. 107(2):208-215.
Babiker, E.M., Gordon, T.C., Chao, S., Rouse, M.N., Brown Guedira, G.L., Pretorius, Z.A., Wanyera, R., Newcomb, M., Bonman, J.M. 2016. Genetic mapping of resistance to the Ug99 race group of Puccinia graminis f. sp tritici in a spring wheat landrace CItr 4311. Theoretical and Applied Genetics. 129(11):2161-2170.
Esvelt Klos, K.L., Huang, Y., Babiker, E.M., Beattie, A., Bekele, W.A., Bjornstad, A., Bonman, J.M., Carson, M.L., Chao, S., Gnanesh, B.N., Harrison, S.A., Howarth, C.J., Hu, G., Ibrahim, A., Islamovic, E., Jackson, E.W., Jannink, J., Kolb, F.L., Mcmullen, M.S., Fetch, J.M., Murphy, J., Obert, D.E., Ohm, H.W., Rines, H.W., Rossnagel, B., Schuleter, J.A., Wight, C.P., Yan, W., Tinker, N.A. 2016. Population genetics related to adaptation in elite oat germplasm. The Plant Genome. 9(2):1-12. doi: 10.3835/plantgenome2015.10.0103.
Mahoney, A., Babiker, E.M., Paulitz, T.C., See, D.R., Okubara, P.A., Hulbert, S. 2016. Characterizing and mapping resistance in synthetic-derived wheat to Rhizoctonia root rot in a green bridge environment. Phytopathology. 106:1170-1176.
Nirmala, J.H., Chao, S., Olivera, P., Babiker, E.M., Abeyo, B., Tadesse, Z., Imtiaz, M., Talbert, L., Blake, N., Akhunov, E., Pumphrey, M.O., Jin, Y., Rouse, M.N. 2016. Markers linked to wheat stem rust resistance gene Sr11 effective to Puccinia graminis f. sp. tritici race TKTTF. Phytopathology. 106(11):1352-1358.
Nirmala, J.H., Chao, S., Olivera, P., Babiker, E.M., Abeyo, B., Tadesse, Z., Imtiaz, M., Talbert, L., Blake, N., Akhunov, E., Pumphrey, M., Rouse, M.N., Jin, Y. 2017. Markers linked to wheat stem rust resistance gene Sr11 effective to Puccinia graminis f. sp. tritici race TKTTF. Phytopathology. 106(11):1352-1358.
Chaffin, A.S., Huang, Y., Smith, S., Bekele, W.A., Babiker, E.M., Gnanesh, B.N., Foresman, B.J., Blanchard, S.G., Jay, J.J., Reid, R.W., Wight, C.P., Chao, S., Oliver, R., Islamovic, E., Kolb, F.L., McCartney, C., Mitchell Fetch, J.W., Beattie, A.D., Bjornstad, A., Bonman, J.M., Langdon, T., Howarth, C.J., Brouwer, C.R., Jellen, E.N., Esvelt Klos, K.L., Poland, J., Hsieh, T., Brown, R., Jackson, E., Schlueter, J.A., Tinker, N.A. 2016. A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial sub-genome rearrangement. The Plant Genome. 9(2). doi: 10.3835/plantgenome2015.10.0102.
Bonman, J.M., Babiker, E.M., Cuesta-Marcos, A., Esvelt Klos, K.L., Brown Guedira, G.L., Chao, S., See, D.R., Chen, J., Akhunov, E., Zhang, J., Bockelman, H.E., Gordon, T.C. 2015. Genetic diversity among wheat accessions from the USDA National Small Grains Collection. Crop Science. 55(3):1243-1253.
Babiker, E.M., Bonman, J.M., Gordon, T.C., Chao, S., Rouse, M.N., Brown Guedira, G.L., Williamson, S., Pretorius, Z.A. 2016. Rapid identification of resistance loci effective against Puccinia graminis f. sp. tritici race TTKSK in 33 spring wheat landraces. Plant Disease. 100(2):331-336.
Babiker, E.M., Bonman, J.M., Gordon, T.C., Chao, S., Newcomb, M.S., Rouse, M.N., Jin, Y., Wanyera, R., Acevedo, M., Brown Guedira, G.L., Williamson, S. 2015. Mapping resistance to the Ug99 race group of the stem rust pathogen in a spring wheat landrace. Journal of Theoretical and Applied Genetics. 128:605-612. doi:10.1007/s00122-015-2456-6. -(Peer Reviewed Journal)
Babiker, E.M., Gordon, T.C., Obert, D.E., Jackson, E.W., Harrison, S.A., Chao, S., Carson, M.L., Bonman, J.M. 2015. Quantitative trait loci from two genotypes of oat (Avena sativa L.) conditioning resistance to Puccinia coronata. Phytopathology. 105(2):239-245.
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