Research Project: Applied Agricultural Genomics and Bioinformatics Research

Location: Genomics and Bioinformatics Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

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.

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.

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.

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.

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.

Intrinsic variation in the vertically transmitted core virome of the mosquito Aedes aegypti - (Peer Reviewed Journal)
Coatsworth, H., Bozic, J., Carillo, J., Buckner, E., Rivers, A.R., Dinglasan, R., Mathias, D. 2022. Intrinsic variation in the vertically transmitted core virome of the mosquito Aedes aegypti. Molecular Ecology. 31(9):2545-2561. https://doi.org/10.1111/mec.16412.

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.

Analysis of a tetraploid cotton line Mac7 transcriptome reveals mechanisms underlying resistance against the whitefly Bemisia tabaci - (Peer Reviewed Journal)
Aslam, M.Q., Naqvi, R.Z., Asif, M., Akhter, K.P., Scheffler, B.E., Scheffler, J.A., Liu, S., Amin, I., Mansoor, S. 2022. Analysis of a tetraploid cotton line Mac7 transcriptome reveals mechanisms underlying resistance against the whitefly Bemisia tabaci. Gene. 820:146200. https://doi.org/10.1016/j.gene.2022.146200.

Advancing equity and inclusion in microbiome research and training - (Peer Reviewed Journal)
Foxx, A., Franco Melendez, K.P., Hariharan, J., Kozik, A., Wattenburger, C., Godoy-Vitorino, F., Rivers, A.R. 2021. Advancing equity and inclusion in microbiome research and training. mSystems. 6(5):e01151-21. https://doi.org/10.1128/mSystems.01151-21.

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.

Identification of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) that are associated with nectariless trait of Gossypium hirsutum L. - (Peer Reviewed Journal)
Park, S., Scheffler, J.A., Ray, J.D., Scheffler, B.E. 2021. Identification of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) that are associated with nectariless trait of Gossypium hirsutum L.. Euphytica. 217:78. https://doi.org/10.1007/s10681-021-02799-8.

Gene disruption by structural mutations drives selection in US rice breeding over the last century - (Peer Reviewed Journal)
Vaughn, J.N., Korani, W., Stein, J.C., Edwards, J., Peterson, D.G., Simpson, S.A., Youngblood, R.C., Grimwood, J., Ware, D., Mcclung, A.M., Scheffler, B.E. 2021. Gene disruption by structural mutations drives selection in US rice breeding over the last century. PLoS Genetics. 17(3): e1009389. https://doi.org/10.1371/journal.pgen.1009389.

Comparison of homogenization methods for extraction of maize cob metabolites - (Peer Reviewed Journal)
Winders, J.R., Pechan, T. 2021. Comparison of homogenization methods for extraction of maize cob metabolites. African Journal of Biotechnology. 20(3):108-114. https://doi.org/10.5897/AJB2020.17246.

Under-the-radar dengue virus infections in natural populations of aedes aegypti mosquitoes - (Peer Reviewed Journal)
Boyles, S., Mavian, C., Finol, E., Ukhanova, M., Stephenson, C., Hamerlinck, G., Kang, S., Baumgartner, C., Geesey, M., Rivers, A.R. 2020. Under-the-radar dengue virus infections in natural populations of aedes aegypti mosquitoes. mSphere. 5(2):e00316-20. https://doi.org/10.1128/mSphere.00316-20.

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.

Whole genome sequencing of Asia II 1 species of whitefly reveals that genes involved in virus transmission and insecticide resistance have genetic variances between Asia II 1 and MEAM1 species - (Peer Reviewed Journal)
Hussain, S., Farooq, M., Malik, H., Amin, I., Scheffler, B.E., Scheffler, J.A., Liu, S., Mansoor, S. 2019. Whole genome sequencing of Asia II 1 species of whitefly reveals that genes involved in virus transmission and insecticide resistance have genetic variances between Asia II 1 and MEAM1 species. BMC Genomics. 20:507. https://doi.org/10.1186/s12864-019-5877-9.

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science - (Peer Reviewed Journal)
Bolyen, E., Rideout, J., Dillon, M., Bokulich, N., Abnet, C., Al-Ghalith, G., Alexander, H., Alm, E., Arumugam, M., Asnicar, F., Rivers, A.R. 2019. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. Nature Biotechnology. https://doi.org/10.1038/s41587-019-0209-9.

Chemical defense responses of upland cotton, Gossypium hirsutum L. to physical wounding - (Peer Reviewed Journal)
Park, S., Scheffler, J.A., Scheffler, B.E., Cantrell, C.L., Pauli, C.S. 2019. Chemical defense responses of upland cotton, Gossypium hirsutum L. to physical wounding. Plant Direct. 3:5. https://doi.org/10.1002/pld3.141.

Crossword: A data-driven simulation language for the design of genetic-mapping experiments and breeding strategies - (Peer Reviewed Journal)
Korani, W., Vaughn, J.N. 2019. Crossword: A data-driven simulation language for the design of genetic-mapping experiments and breeding strategies. bioRxiv. 9:4386. http://dx.doi.org/10.1101/330563.

ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis - (Peer Reviewed Journal)
Rivers, A.R., Weber, K.C., Gardner, T.G., Liu, S., Armstrong, S. 2018. ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Research. 7:1418. https://doi.org/10.12688/f1000research.15704.1.

Differential Gene Expression of Southern Highbush Blueberry cv. ‘O’Neal’ Floral Buds in Response to Freeze Treatment and Recovery Periods - (Abstract Only)

RNA-Seq Analysis of Floral Bud Response to Freeze Treatments in Southern Highbush Blueberry CV. ‘O’Neal’ - (Abstract Only)