Research Project: Integrated Crop Disease Mitigation through Improved Understanding of Relationships between Genetics, Environment, and Management

Location: Soil Dynamics Research

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

Metatranscriptomic characterization of the cotton aphid (Aphis gossypii) virome reveals broad viral diversity and novel Iflavirus species - (Peer Reviewed Journal)
Zhao, C., Owens, I., Jacobson, A.L., Escalante, C., Bansal, R., Martin, K.M., Balkcom, K.S. 2026. Metatranscriptomic characterization of the cotton aphid (Aphis gossypii) virome reveals broad viral diversity and novel Iflavirus species. BMC Genomics. 2026. https://doi.org/10.1186/s12864-026-13132-9.

Bee (Hymenoptera) bycatch assemblages collected in bowl traps at interfaces of cotton agroecosystems in Alabama - (Peer Reviewed Journal)
Mahas, J.B., Abbate, A.P., Mahas, J.W., Ray, C., Jacobson, A. 2026. Bee (Hymenoptera) bycatch assemblages collected in bowl traps at interfaces of cotton agroecosystems in Alabama. Environmental Entomology. 55(2):nvag037. https://doi.org/10.1093/ee/nvag037.

First molecular verification of the two-spot cotton leafhopper Amrasca biguttula (Hemiptera: Cicadellidae) in the United States - (Peer Reviewed Journal)
Zhao, C., Balkcom, K.S. 2026. First molecular verification of the two-spot cotton leafhopper Amrasca biguttula (Hemiptera: Cicadellidae) in the United States. Insects. 17(3):313. https://doi.org/10.3390/insects17030313.

Metatranscriptomics analysis reveals the cotton virome in the southern United States - (Peer Reviewed Journal)
Escalante, C., Reyes, A.M., Zhao, C., Balkcom, K.S., Jacobson, A.L., Strayer-Scherer, A., Martin, K.M., Koebernick, J., Huseth, A., Koziel, E., Small, I., Greene, J., Otulak-Koziel, K., Mulvaney, M.J., Price, P.P., Alcalá Briseño, R.I., Bag, S., Conner, K. 2026. Metatranscriptomics analysis reveals the cotton virome in the southern United States. Scientific Reports. (2026). https://doi.org/10.1038/s41598-026-40828-5.

Cotton-dominated landscapes, vector abundance, and temperature influence cotton leafroll dwarf virus incidence in cotton - (Peer Reviewed Journal)
Mahas, J.W., Roberts, P.M., Conner, K., Graham, S., Huseth, A.S., Steury, T.D., Mahas, J.B., Bag, S., Bowen, K., Jacobson, A.L. 2026. Cotton-dominated landscapes, vector abundance, and temperature influence cotton leafroll dwarf virus incidence in cotton. Phytopathology. 116(6):942-953. https://doi.org/10.1094/PHYTO-10-25-0349-R.

Gene expression patterns following aphid-mediated polerovirus transmission highlight differences between vector–host and host–virus interactions - (Peer Reviewed Journal)
Pandey, S., Catto, M., Roberts, P., Bad, S., Jacobson, A., Srinivasan, R. 2026. Gene expression patterns following aphid-mediated polerovirus transmission highlight differences between vector–host and host–virus interactions . Phytopathology. 116:825-841. https://doi.org/10.1094/PHYTO-08-25-0283-R.

Data collection and transcriptome analysis of Triticum aestivum samples from Alabama revealed the presence of barley yellow dwarf virus - (Peer Reviewed Journal)
Livingston, R.M., Mayfield, M., Zhao, C., Potnis, N., Strayer-Scherer, A., Martin, K.M. 2025. Data collection and transcriptome analysis of Triticum aestivum samples from Alabama revealed the presence of barley yellow dwarf virus. Frontiers in Agronomy. 7:1721047. https://doi.org/10.3389/fagro.2025.1721047.

Association of plant pathogen vectors and vector-borne plant pathogens with landscape composition: a meta-analysis - (Peer Reviewed Journal)
Mahas, J., Wilson, A.E., Steury, T., Jacobson, A. 2025. Association of plant pathogen vectors and vector-borne plant pathogens with landscape composition: a meta-analysis. Journal of Applied Ecology. 55(1):nvaf120. https://doi.org/10.1093/ee/nvaf120.

Effects of cotton leafroll dwarf virus infection in cotton grown in high heat conditions - (Peer Reviewed Journal)
Schlarbaum, K., Rossi, G., Conner, K.N., Escalante, C., Balkcom, K.S., Lawrence, K.S., Martin, K.M., Jacobson, A.L. 2026. Effects of cotton leafroll dwarf virus infection in cotton grown in high heat conditions. PhytoFrontiers. 6:129-138. https://doi.org/10.1094/PHYTOFR-06-25-0060-R.

The effect of neonicotinoids on thrips oviposition, immatures, and cotton injury - (Peer Reviewed Journal)
Mahas, J., Rossi, G., Chitturi, A., Chaves-Cordoba, B., Graham, S., Jacobson, A. 2025. The effect of neonicotinoids on thrips oviposition, immatures, and cotton injury. Journal of Cotton Science. 29(2):77-86. https://doi.org/10.56454/GQRL7530.

First molecular verification of the cotton jassid (Amrasca biguttula) in the United States - (Rapid Release Publication)
Zhao, C., Balkcom, K.S. 2025. First molecular verification of the cotton jassid (Amrasca biguttula) in the United States. bioRxiv. 2025.09.03.673823. https://doi.org/10.1101/2025.09.03.673823.

Cotton contains multitudes: A metatranscriptomics sequencing approach reveals the cotton virome in the southern United States - (Abstract Only)
Escalante, C., Reyes, A.M., Zhao, C., Jacobson, A., Balkcom, K.S., Conner, K. 2025. Cotton contains multitudes: A metatranscriptomics sequencing approach reveals the cotton virome in the southern United States [abstract]. Phytopathology 114:S1.28. https://doi.org/10.1094/PHYTO-114-11-S1.1.

Unveiling viral diversity in Aphis gossypii: Discovery and characterization of novel Iflaviruses - (Abstract Only)
Owens, I.M., Zhao, C. 2025. Unveiling viral diversity in Aphis gossypii: Discovery and characterization of novel Iflaviruses [abstract]. 2025 Plants, Insects and Microbes Symposium, Auburn, AL. May 20, 2025.

Identification of candidate host-manipulating effector genes in Aphis gossypii (Hemiptera: Aphididae) using a combination of transcriptome, genome, and differential gene expression data - (Peer Reviewed Journal)
Zhao, C., Mueller, N., Owens, I., Bansal, R., Jacobson, A.L. 2025. Identification of candidate host-manipulating effector genes in Aphis gossypii (Hemiptera: Aphididae) using a combination of transcriptome, genome, and differential gene expression data. Journal of Insect Science. 25(3):11. https://doi.org/10.1093/jisesa/ieaf053.

Identification key for cotton-feeding aphids (Hemiptera: Aphididae) found in pan traps in the Southeast - (Peer Reviewed Journal)
Mahas, J., Ray, C., Hamilton, F., Miller, G.L., Jacobson, A. 2025. Identification key for cotton-feeding aphids (Hemiptera: Aphididae) found in pan traps in the Southeast. Florida Entomologist. 108:20240012. https://doi.org/10.1515/flaent-2024-0012.

Metatranscriptomic and metagenomic analyses of cotton aphids (Aphis gossypii) collected from cotton fields in Alabama, USA - (Peer Reviewed Journal)
Zhao, C., Escalante, C., Jacobson, A.L., Balkcom, K.S., Conner, K.N., Martin, K.M. 2025. Metatranscriptomic and metagenomic analyses of cotton aphids (Aphis gossypii) collected from cotton fields in Alabama, USA. Frontiers in Insect Science. 5:1461588. https://doi.org/10.3389/finsc.2025.1461588.

Identification of candidate plant-manipulating effector genes in the cotton aphid, Aphis gossypii - (Abstract Only)

Data and code from: Cotton stalk management and a cover crop produce minimal effects on cotton leafroll dwarf virus - (Database / Dataset)
Balkcom, K.S., Read, Q.D., Frazier, S., Brown, S., Jacobson, A.L., Conner, K., Escalante, C. 2024. Data and code from: Cotton stalk management and a cover crop produce minimal effects on cotton leafroll dwarf virus. Ag Data Commons. Software. https://doi.org/10.15482/USDA.ADC/25783143.

Cotton stalk management and a cover crop produce minimal effects on cotton leafroll dwarf virus - (Peer Reviewed Journal)
Frazier, S., Brown, S.M., Read, Q.D., Jacobson, A.L., Conner, K., Escalante, C., Balkcom, K.S. 2024. Cotton stalk management and a cover crop produce minimal effects on cotton leafroll dwarf virus. Agronomy Journal. 117(1):e70002. https://doi.org/10.1002/agj2.70002.

Decoding the viral community in soybean thrips (Neohydatothrips variabilis) through RNA-Seq suggests presence of insect, plant and fungal viruses in Auburn, AL, 2023 - (Abstract Only)
Sharma, A., Zhao, C., Martin, K.M. 2025. Decoding the viral community in soybean thrips (Neohydatothrips variabilis) through RNA-Seq suggests presence of insect, plant and fungal viruses in Auburn, AL, 2023 [abstract]. 2025 Beltwide Cotton Conferences, New Orleans, LA. Jan 14-16, 2025.

Transcriptomic analysis of salivary glands in the cotton aphid, Aphis gossypii - (Abstract Only)
Zhao, C., Escalante, C., Jacobson, A.L. 2024. Transcriptomic analysis of salivary glands in the cotton aphid, Aphis gossypii [abstract]. 2024 Entomological Society of America (ESA) Annual Meetings, Phoenix, AZ. Nov. 10-13, 2024.

Characterization of the proteins encoded by a recently emerged cotton-infecting Polerovirus - (Peer Reviewed Journal)
Akinyuwa, M., Price, B., Kang, S. 2024. Characterization of the proteins encoded by a recently emerged cotton-infecting Polerovirus. Virus Genes. https://doi.org/10.1007/s11262-024-02086-3.

Monitoring the distribution, incidence, and symptom expression associated with cotton leafroll dwarf virus in the southern United States using a sentinel plot system - (Peer Reviewed Journal)
Koebernick, J.C., Hagan, A.K., Zaccaron, M., Escalante, C., Jacobson, A.L., Bowen, K.L., Strayer-Scherer, A., Heilsnis, B., Brown, S., Sikora, E.J., Allen, T.W., Faske, T.R., Bourland, F., Greene, J.K., Huseth, A., Kelly, H., Kemerait, R.C., Kerns, D., Mulvaney, M., Price, P.P., Small, I., Taylor, S., Wang, H., Conner, K. 2024. Monitoring the distribution, incidence, and symptom expression associated with cotton leafroll dwarf virus in the southern United States using a sentinel plot system. PhytoFrontiers. 4(4):671–681. https://doi.org/10.1094/PHYTOFR-02-24-0008-R.

Investigating the interaction of plant age and timing of cotton leafroll dwarf virus infection on yield loss - (Peer Reviewed Journal)
Schlarbaum, K., Conner, K., Roberts, P., Toews, M., Jacobson, A. 2025. Investigating the interaction of plant age and timing of cotton leafroll dwarf virus infection on yield loss. Journal of Cotton Science. 29:225-234. https://doi.org/10.56454/SAML3448.

Plant virus transmission during seed development and implications to plant defense system - (Peer Reviewed Journal)
Escalante, C., Sanz-Seaz, A., Jacobson, A., Otulak-Koziel, K., Koziel, E., Balkcom, K.S., Zhao, C., Conner, K. 2024. Plant virus transmission during seed development and implications to plant defense system. Frontiers in Plant Science. 15:1385456. https://doi.org/10.3389/fpls.2024.1385456.

Yeast two-hybrid screening for cotton leafroll dwarf virus-Aphis gossypii interactions - (Abstract Only)
Mueller, N., Zhao, C. 2024. Yeast two-hybrid screening for cotton leafroll dwarf virus-Aphis gossypii interactions. Plants, Insects and Microbes Symposium, Auburn, AL. May 17, 2024.

A newly isolated cotton-infecting Polerovirus with cryptic pathogenicity encodes a weak suppressor of RNA silencing - (Peer Reviewed Journal)
Akinyuwa, M., Price, B., Martin, K., Kang, S. 2023. A newly isolated cotton-infecting Polerovirus with cryptic pathogenicity encodes a weak suppressor of RNA silencing. Frontiers in Agronomy. 5:1235168. https://doi.org/10.3389/fagro.2023.1235168.

Effects of cotton stalk management and cover crop use on soil properties and CLRDV incidence - (Abstract Only)
Frazier, S., Brown, S., Balkcom, K.S., Jacobson, A.L. 2022. Effects of cotton stalk management and cover crop use on soil properties and CLRDV incidence [ABSTRACT]. In S. Boyd and M. Huffman (eds.) Beltwide Cotton Conf., San Antonio, TX. 4-6 Jan. 2022 Nat. Cotton Counc. Cordova, TN.