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Amanda Hulse-Kemp
Computational Biologist
Computational Biologist
Phone: (919) 515-7599
Dept of Crop and Soil Sciences
CB 7620, Room 1244
Raleigh, 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.
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- Hypothalamic Transcriptome Response To Simulated Diel Earthen Pond Hypoxia Cycles In Channel Catfish (Ictalurus punctatus) -(Peer Reviewed Journal)
Ott, B.D., Torrans, E.L., Griffins, M.J., Allen, P.J., Duke, M.V., Peterson, B.C., Scheffler, B.E., Hulse-Kemp, A.M. 2024. Hypothalamic Transcriptome Response To Simulated Diel Earthen Pond Hypoxia Cycles In Channel Catfish (Ictalurus punctatus). Physiological Genomics. https://doi.org/10.1152/physiolgenomics.00007.2024.
- Two haplotype-resolved genomes of Hydrangea macrophylla reveal important flower traits for breeding improvement-(Proceedings)
- A blueberry (Vaccinium spp.) crop ontology to enable standardized phenotyping for blueberry breeding and research -(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. - Gossypium hirsutum gene Gohir.A02G161000.1 encodes a potential Root UVB Sensitive Protein with a putative protein-protein interaction interface -(Peer Reviewed Journal)
Brocker, D., Cutlan, M., Hulse-Kemp, A.M., Storm, A.R., Stoeckman, A.K. 2024. Gossypium hirsutum gene Gohir.A02G161000.1 encodes a potential Root UVB Sensitive Protein with a putative protein-protein interaction interface. microPublication Biology. https://doi.org/10.17912/micropub.biology.000869. - Developing a new crop ontology for blueberry-(Abstract Only)
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. - Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea (Hydrangea macrophylla) and insights into Asterid evolution -(Peer Reviewed Journal)
Wu, X., Simpson, S.A., Youngblood, R., Scheffler, B.E., Alexander, L.W., Hulse-Kemp, A.M. 2023. Whole genome sequencing reveals genes implicated with important flower traits in bigleaf hydrangea (Hydrangea macrophylla). Horticulture Research. https://doi.org/10.1093/hr/uhad217. - Representing true plant genomes: haplotype-resolved hybrid pepper genome through trio binning -(Peer Reviewed Journal)
Delorean, E.E., Youngblood, R.C., Simpson, S.A., Schoonmaker, A.N., Scheffler, B.E., Rutter, W.B., Hulse-Kemp, A.M. 2023. Representing true plant genomes: haplotype-resolved hybrid pepper genome through trio binning. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2023.1184112. - Gossypium hirsutum gene of unknown function, Gohir.A02G039501.1, encodes a potential DNA-binding ALOG protein involved in gene regulation -(Peer Reviewed Journal)
Zirkel, J., Hulse-Kemp, A.M., Storm, A.R. 2023. Gossypium hirsutum gene of unknown function, Gohir.A02G039501.1, encodes a potential DNA-binding ALOG protein involved in gene regulation. microPublication Biology. https://doi.org/10.17912/micropub.biology.000670. - Gossypium hirsutum gene of unknown function Gohir.A03G0737001
encodes a potential chaperone-like protein of protochlorophyllide
oxidoreductase (CPP1) -(Peer Reviewed Journal)
Osagiede, A., Osborne, A.N., Hulse-Kemp, A.M., Storm, A.R., Stoeckman, A.K. 2023. Gossypium hirsutum gene of unknown function Gohir.A03G0737001 encodes a potential chaperone-like protein of protochlorophyllide oxidoreductase (CPP1). microPublication Biology. https://doi.org/10.17912/micropub.biology.000867. - 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. - Genetics of destemming in pepper: A step towards mechanical harvesting -(Peer Reviewed Journal)
Hill, T., Cassibba, V., Joukhadar, I., Tonnessen, B., Havlik, C., Ortega, F., Sripolcharoen, S., Visser, B.J., Stoffel, K., Thammapichai, P., Garcia-Llanos, A., Chen, S., Hulse-Kemp, A.M., Walker, S., Van Deynze, A. 2023. Genetics of destemming in pepper. Frontiers in Genetics. https://doi.org/doi:10.3389/fgene.2023.1114832. - Gossypium hirsutum gene of unknown function Gohir.A03G007700.1 encodes a potential VAN3-binding protein with a phosphoinositide-binding site -(Peer Reviewed Journal)
Smith, E.R., Caulley, L.R., Hulse-Kemp, A.M., Storm, A.R., Stoeckman, A.K. 2023. Gossypium hirsutum gene of unknown function Gohir.A03G007700.1 encodes a potential VAN3-binding protein with a phosphoinositide-binding site. microPublication Biology. https://doi.org/10.22002/rf8g5-hm387. - 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. - Efficient imaging and computer vision detection of two cell shapes in young cotton fibers -(Peer Reviewed Journal)
Graham, B.P., Park, J., Billings, G.T., Hulse-Kemp, A.M., Haigler, C.H., Lobaton, E. 2022. Efficient imaging and computer vision detection of two cells in young cotton fibers. Applications in Plant Sciences. https://doi.org/10.1002/aps3.11503. - 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)
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