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                    U.S. DEPARTMENT OF AGRICULTURE
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Amanda  Hulse-Kemp    Computational Biologist Phone: (919) 515-7599 Dept of Crop and Soil SciencesCB 7620, Room 1244Raleigh, NC 27695 Amanda is a Computational Biologist with the United States Department of Agriculture – Agriculture Research Service in the Genomics and Bioinformatics Research Unit and is located in Raleigh, NC on the North Carolina State University campus. She obtained her Ph.D. from Texas A&M University working on identification and integration of sequence-based markers for breeders in cotton for which she received numerous awards. Her postdoctoral research at the University of California, Davis focused on bioinformatics, resource development and integration of genomics and biotechnology tools for enhancing breeding of vegetables and other crops including spinach, cotton, tomato, coffee and pepper. Current research interests involve utilizing bioinformatics to intelligently enhance ARS breeding programs in both crops and animals.  ProjectsGenomic Selection is Looming: Building a Robust Genotype-to-Phenotype Platform to Revolutionize Public Cotton BreedingCooperative Agreement (A)Accession Number:441704Genomic Selection is Looming: Building a Robust Genotype-to-Phenotype Platform to Revolutionize Public Cotton BreedingCooperative Agreement (A)Accession Number:443680Integrative Applied Agricultural ‘Omics and Bioinformatics ResearchIn-House Appropriated (D)Accession Number:444279Genomic Selection is Looming: Building a Robust Genotype-to-Phenotype Platform to Revolutionize Public Cotton BreedingInteragency Reimbursable Agreement (I)Accession Number:441416Developing a Haplotype-assisted Breeding System for Upland Cotton - StonevilleInteragency Reimbursable Agreement (I)Accession Number:443312Advancing U.S. and Peru Relations Through Collaborative Genomics Research of Mutually Important Agricultural CropsNon-Funded Cooperative Agreement (N)Accession Number:436828Improving the Drought Tolerance and Sustainability of Turfgrasses Used in Southern Landscapes Through the Integration of Breeding, Genetics,...Reimbursable Cooperative Agreement (R)Accession Number:437576Modernizing Cotton and Other Crop Breeding Systems by Integrating Genomic AnalysesNon-Assistance Cooperative Agreement (S)Accession Number:438571Coordinating Breeding Informatics to Benefit Specialty CropsNon-Assistance Cooperative Agreement (S)Accession Number:438590Building Genomic Resources and Investigating Traits in Grass SpeciesNon-Assistance Cooperative Agreement (S)Accession Number:438739Machine Learning Integration into Breeding ProgramsNon-Assistance Cooperative Agreement (S)Accession Number:440876Breeding Informatics to Benefit AgricultureNon-Assistance Cooperative Agreement (S)Accession Number:437029USDA ARS Research Apprenticeship Program at University of Texas at ArlingtonNon-Assistance Cooperative Agreement (S)Accession Number:442862Utilization of Cutting Edge Real Time Sensor Technology in Sugarcane BreedingNon-Assistance Cooperative Agreement (S)Accession Number:444548Building Tools for Specialty Crop Breeding ProgramsNon-Assistance Cooperative Agreement (S)Accession Number:444871Developing Intelligent Tools for High-throughput Crop PhenotypingNon-Assistance Cooperative Agreement (S)Accession Number:444993  Publications(Clicking on the reprint iconReprint Icon  will take you to the publication reprint.)Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa-(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.A first look at the ability to use genomic prediction for improving ratooning ability of sugarcane-(Peer Reviewed Journal) Islam, M.S., Corak, K., Mccord, P.H., Hulse-Kemp, A.M., Lipka, A.E. 2023. A first look at the ability to use genomic prediction for improving ratooning ability of sugarcane. Frontiers in Plant Science. 14. https://doi.org/10.3389/fpls.2023.1205999.Detecting cotton leaf curl virus resistance quantitative trait Loci in Gossypium hirsutum and iCottonQTL a new R/Shiny app to streamline genetic mapping in cotton-(Peer Reviewed Journal) Schoonmaker, A., Hulse-Kemp, A.M., Youngblood, R.C., Rahmat, M., Iqbal, M., Mehboob-Ur-, R., Kochan, K.J., Scheffler, B.E., Scheffler, J.A. 2023. Detecting cotton leaf curl virus resistance quantitative trait Loci in Gossypium hirsutum and iCottonQTL a new R/Shiny app to streamline genetic mapping in cotton. Plants.  https://doi.org/10.3390/plants12051153.Two pathogen loci determine Blumeria graminis f. sp. tritici virulence
to wheat resistance gene Pm1a-(Peer Reviewed Journal) Kloppe, T., Whetten, R.B., Kim, S., Powell, O., Luck, S., Douchkov, D., Whetten, R., Hulse-Kemp, A.M., Balint Kurti, P.J., Cowger, C. 2023. Two pathogen loci determine Blumeria graminis f. sp. tritici virulence to wheat resistance gene Pm1a. New Phytologist. 238:1546-1561. https://doi.org/10.1111/nph.18809.Initiation of genomics-assisted breeding in virginia-type peanuts through the generation of a de novo reference genome and informative markers-(Peer Reviewed Journal) Newman, C.S., Andres, R.J., Youngblood, R.C., Campbell, J.D., Simpson, S.A., Cannon, S.B., Scheffler, B.E., Oakley, A.T., Hulse-Kemp, A.M., Dunne, J.C. 2023. Initiation of genomics-assisted breeding in Virginia-type peanuts through the generation of a de novo reference genome and informative markers. Frontiers in Plant Science. 13.Article 1073542. https://doi.org/10.3389/fpls.2022.1073542.Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon-(Peer Reviewed Journal) Vaughn, J.N., Branham, S.E., Abernathy, B.L., Hulse-Kemp, A.M., Rivers, A.R., Levi, A., Wechter, W.P. 2022. Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon. Nature Genetics. https://doi.org/10.1038/s41467-022-35621-7.Genetic variability and QTL mapping of winter survivability and leaf firing in African bermudagras-(Peer Reviewed Journal) Yu, S., Schoonmaker, A., Yan, L., Hulse-Kemp, A.M., Fontanier, C.H., Martin, D.L. 2022. Genetic variability and QTL mapping of winter survivability and leaf firing in African bermudagras. Crop Science.  https://doi.org/10.1002/csc2.20849.Gossypium hirsutum gene of unknown function, Gohir.A02G044702.1, encodes a potential B3 transcription factor of the REM subfamily-(Peer Reviewed Journal) Allen, M., Hulse-Kemp, A.M., Storm, A.R. 2022. Gossypium hirsutum gene of unknown function, Gohir.A02G044702.1, encodes a potential B3 transcription factor of the REM subfamily. microPublication Biology. https://doi.org/10.17912/micropub.biology.000574.Outlook for implementation of genomics-based selection in public cotton breeding programs-(Peer Reviewed Journal) Billings, G.T., Jones, M.A., Rustgi, S., Bridges, W.C., Holland, J.B., Hulse-Kemp, A.M., Campbell, B.T. 2022. Outlook for implementation of genomics-based selection in public cotton breeding programs. Plants. 11(11). https://doi.org/10.3390/plants11111446.Chromosome-scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication-(Peer Reviewed Journal) Chang, J., Marczuk-Rojas, J.P., Waterman, C., Garcia-Llanos, A., Chen, S., Ma, X., Hulse-Kemp, A.M., Van Deynze, A., Van De Peer, Y., Carretero-Paulet, L. 2022. Chromosome-scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication. The Plant Genome.  https://doi.org/10.1002/tpg2.20238.There and back again; historical perspective and future directions for Vaccinium breeding and research studies-(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.Leveraging national germplasm collections to determine significantly associated categorical traits in crops: Upland and Pima Cotton as a case study-(Peer Reviewed Journal) Restrepo-Montoya, D., Hulse-Kemp, A.M., Scheffler, J.A., Haigler, C., Hinze, L.L., Love, J., Percy, R.G., Jones, D.C., Frelichowski, J.E. 2022. Leveraging national germplasm collections to determine significantly associated categorical traits in crops: Upland and Pima Cotton as a case study. Frontiers in Plant Science. 13:837038. https://doi.org/10.3389/fpls.2022.837038.The spinach YY genome reveals sex chromosome evolution, domestication, and introgression history of the species-(Peer Reviewed Journal) Ma, X., Yu, L., Fatima, M., Wadlington, W.H., Hulse-Kemp, A.M., Zhang, X., Zhang, S., Xu, X., Van Deynze, A., Ming, R. 2022. Sex chromosome evolution, domestication and introgression history revealed by a YY genome in spinach. Genome Biology. https://doi.org/10.1186/s13059-022-02633-x.Nuclear DNA contents and ploidy levels of North American Vaccinium species and interspecific hybrids-(Peer Reviewed Journal) Redpath, L., Aryal, R., Lynch, N., Spencer, J.A., Hulse-Kemp, A.M., Ballington, J.R., Green, J., Bassil, N.V., Hummer, K.E., Ranney, T., Ashrafi, H. 2022. Nuclear DNA contents and ploidy levels of North American Vaccinium species and interspecific hybrids. Scientia Horticulturae. 297. Article 110955. https://doi.org/10.1016/j.scienta.2022.110955.Turfgrass genome sequencing from the USDA-ARS turfgrass consortium-(Abstract Only)High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii)-(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.Population structure and genetic diversity of the Pee Dee cotton breeding program-(Peer Reviewed Journal) Billings, G., Jones, M., Rustgi, S., Hulse-Kemp, A.M., Campbell, B.T. 2021. Population structure and genetic diversity of the Pee Dee cotton breeding program. Genes, Genomes, Genetics. https://doi.org/10.1093/g3journal/jkab145.An anchored chromosome-scale genome assembly of spinach (Spinacia oleracea) improves annotation and reveals extensive gene rearrangements in euasterids-(Peer Reviewed Journal) Hulse-Kemp, A.M., Bostan, H., Chen, S., Ashrafi, H., Iorizzo, M., Van Deynze, A. 2021. An anchored chromosome-scale genome assembly of spinach (Spinacia oleracea) improves annotation and reveals extensive gene rearrangements in euasterids. The Plant Genome. 14(2):e20137. https://doi.org/10.1002/tpg2.20137.Genomic resource development for hydrangea (Hydrangea macrophylla (Thunb.) Ser.) – A transcriptome assembly and a high-density genetic linkage map-(Peer Reviewed Journal) Wu, X., Hulse-Kemp, A.M., Wadl, P.A., Smith, Z., Mockaitis, K., Staton, M.E., Rinehart, T.A., Alexander, L.W. 2021. Genomic resource development for hydrangea (Hydrangea macrophylla (Thunb.) Ser.) – A transcriptome assembly and a high-density genetic linkage map. Horticulturae. https://doi.org/10.3390/horticulturae7020025.Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement-(Peer Reviewed Journal) Chen, Z., Sreedasyam, A., Ando, A., Song, Q., De Santiago, L., Hulse-Kemp, A.M., Ding, M., Ye, W., Kirkbride, R., Jenkins, J., Plott, C., Lovell, J., Yu-Ming, L., Vaughn, R., Liu, B., Simpson, S.A., Scheffler, B.E. 2020. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nature Genetics. https://doi.org/10.1038/s41588-020-0614-5.Transcriptional analyses of differential cultivars during resistant and susceptible interactions with Peronospora effusa, the causal agent of spinach downy mildew-(Peer Reviewed Journal) Kandel, S.L., Hulse-Kemp, A.M., Stoffel, K., Koike, S.T., Shi, A., Mou, B., Van Deynze, A., Klosterman, S.J. 2020. Transcriptional analyses of differential cultivars during resistant and susceptible interactions with Peronospora effusa, the causal agent of spinach downy mildew. Scientific Reports. 10. Article 6719. https://doi.org/10.1038/s41598-020-63668-3.Enhancing upland cotton for drought resilience, productivity and fiber quality: Comparative evaluations and genetic dissection-(Peer Reviewed Journal) Ulloa, M., De Santiago, L., Hulse-Kemp, A.M., Stellly, D.M., Burke, J.J. 2019. Enhancing upland cotton for drought resilience, productivity and fiber quality: Comparative evaluations and genetic dissection. Molecular Genetics and Genomics. 295(1):155-176. https://doi.org/10.1007/s00438-019-01611-6.Capsicum - an abbreviated compendium-(Peer Reviewed Journal) Jarret, R.L., Barboza, G., Batista, F., Chou, Y., Hulse-Kemp, A.M., Ochoa-Alejo, N., Veres, A., Berke, T., Carrizo, C., Csillery, G., Huang, Y., Kiss, E., Kovacs, Z., Kondrak, M., Arce-Rodriguez, M., Scaldaferro, M.A., Szoke, A., Tripodi, P. 2019. Capsicum - an abbreviated compendium. Journal of the American Society for Horticultural Science. 144(1):3-22. https://doi.org/10.21273/JASHS04446-18.Feeding high-oleic peanuts to layer hens enhances egg yolk color and oleic fatty acid content in shell eggs-(Peer Reviewed Journal) Toomer, O.T., Hulse-Kemp, A.M., Dean, L.L., Boykin, D.L., Ramon, M., Anderson, K.E. 2019. Feeding high-oleic peanuts to layer hens enhances egg yolk color and oleic fatty acid content in shell eggs. Poultry Science. 98:1732-1748. https://doi.org/10.3382/ps/pey531.Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitive Trait Loci Detection-(Peer Reviewed Journal) Gonda, I., Ashrafi, H., Lyon, S., Strickler, S., Hulse-Kemp, A.M., Thannhauser, T.W., Mueller, L., Fei, Z., Foolad, M., Giovannoni, J.J., Ma, Q., Sun, H., Stoffel, K., Powell, A., Futrell, S., Van Deynze, A. 2018. A GBS-based high-density genetic map of a tomato RIL population facilitating high resolution QTL mapping and candidate gene identification. The Plant Genome. 12:1. https://doi.org/10.3835/plantgenome2018.02.0010.Differential Gene Expression of Southern Highbush Blueberry cv. ‘O’Neal’ Floral Buds in Response to Freeze Treatment and Recovery Periods-(Abstract Only)A Spinach Genome for the Next Generation of Breeders-(Abstract Only)RNA-Seq Analysis of Floral Bud Response to Freeze Treatments in Southern Highbush Blueberry CV. ‘O’Neal’-(Abstract Only)Comparative transcriptomics and genomics patterns of discordance in Capsiceae (Solanaceae)-(Peer Reviewed Journal) Spalink, D., Stoffel, K., Hill, T.A., Hulse-Kemp, A.M., Walden, G., Van Deynze, A., Bohs, L. 2018. Comparative transcriptomics and genomics patterns of discordance in Capsiceae (Solanaceae). Systematic Biology. 126(2018):293-302. https://doi: 10.1016/j.ympev.2018.04.030.Maximizing Utility of Community-based Resources-(Abstract Only)Lessons from Cotton: Research Projects Following Development of a Community-based Genotyping Array-(Abstract Only)Reference quality assembly of the 3.5 Gb genome of Capsicum annuum form a single linked-read library-(Peer Reviewed Journal) Hulse-Kemp, A.M., Maheshwari, S., Stoffel, K., Hill, T.A., Jaffe, D., Williams, S., Weisenfeld, N., Ramakrishnan, S., Kumar, V., Shah, P., Schatz, M.C., Church, D.M., Van Deynze, A. 2018. Reference quality assembly of the 3.5 Gb genome of Capsicum annuum form a single linked-read library. Horticulture Research. 5(4). https://doi: 10.1038/s41438-017-0011-0.Setting the Stage for California Coffee Farming-(Abstract Only)  ARS News ArticlesitemUSDA's Agricultural Research Service Honors Scientists of the Year


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