Research Project: Improving Fruit Crop Traits Through Advanced Genomic, Breeding, and Management Technologies

Location: Innovative Fruit Production, Improvement, and Protection

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

Temporal changes in the proanthocyanidins to anthocyanins ratio during dormancy associate with bloom time variations in peach - (Peer Reviewed Journal)
Rani Das, P., Islam, M., Liu, J., Liu, Z., Dardick, C.D., Sherif, S. 2024. Temporal changes in the proanthocyanidins to anthocyanins ratio during dormancy associate with bloom time variations in peach. Plant Physiology. 40. https://doi.org/10.1016/j.cpb.2024.100393.

A novel and efficient Agrobacterium-mediated transient gene expression in citrus epicotyls and mature stem tissues - (Peer Reviewed Journal)

Ectopic enhancer–enhancer interactions as causal forces driving RNA-directed DNA methylation in gene regulatory regions - (Peer Reviewed Journal)
Yang, Y., Liu, J., Singer, S., Yan, G., Bennett Jr, D.R., Liu, Y., Wang, X., Hilly, J., Xu, W., Yang, Y., Zhong, G., Liu, Z., An, Y., Liu, H., Liu, Z. 2024. Ectopic enhancer–enhancer interactions as causal forces driving RNA-directed DNA methylation in gene regulatory regions. Plant Biotechnology. https://doi.org/10.1111/pbi.14435.

A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus - (Peer Reviewed Journal)
Mansfeld, B., Yocca, A., Ou, S., Harkness, A., Burchard, E.A., Gutierrez, B.L., Van Nocker, S., Gottschalk, C.C. 2023. A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. The Plant Journal. https://doi.org/10.1111/tpj.16433.

Comparison of red raspberry and wild strawberry fruits reveals mechanisms of fruit type specification - (Peer Reviewed Journal)
Zhou, J., Li, M., Li, Y., Xiao, Y., Li, X., Gao, S., Sadowski, N., Timp, W., Dardick, C.D., Callahan, A.M., Mount, S., Liu, Z. 2023. Comparison of red raspberry and wild strawberry fruits reveals mechanisms of fruit type specification. Plant Physiology. 193(2):1016-1035. https://doi.org/10.1093/plphys/kiad409.

A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus - (Pre-print Publication)
Mansfeld, B., Yocca, A., Ou, S., Harkness, A., Burchard, E.A., Gutierrez, B.L., Van Nocker, S., Gottschalk, C.C. 2023. A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. bioRxiv. https://doi.org/10.1101/2023.03.22.533842.

Conservation and divergence of expression of GA2-oxidase homeologs in apple (Malus x domestica Borkh) - (Peer Reviewed Journal)
Zhang, S., Gottschalk, C.C., Van Nocker, S. 2023. Conservation and divergence of expression of GA2-oxidase homeologs in apple (Malus x domestica Borkh) . Frontiers in Plant Science. 14:1117069. https://doi.org/10.3389/fpls.2023.1117069.

‘Bell’ pear - (Peer Reviewed Journal)
Bell, R., Schuup, J., Dardick, C.D., Demuth, M.A., Gottschalk, C.C. 2023. ‘Bell’ pear. HortScience. 58(8):832-835. https://doi.org/10.21273/HORTSCI17113-23.

Malus species with diverse bloom times exhibit variable rates of floral development - (Peer Reviewed Journal)
Goeckeritz, C., Gottschalk, C.C., Hollender, C., Van Nocker, S. 2023. Malus species with diverse bloom times exhibit variable rates of floral development. Journal of the American Society for Horticultural Science. 148:2. https://doi.org/10.21273/JASHS05236-22.

Improved genome assembly resource of the plant pathogen Fusarium avenaceum - (Peer Reviewed Journal)
Gottschalk, C.C., Evans, B.E., Collum, T.D. 2023. Improved genome assembly resource of the plant pathogen Fusarium avenaceum. American Phytopathological Society. https://doi.org/10.1094/PHYTOFR-10-22-0117-A.

CW198 acts as a genetic insulator to block enhancer-promoter interaction in plants - (Peer Reviewed Journal)
Jiang, L., Liu, Y., Wen, Z., Yang, Y., Singer, S., Bennett Jr, D.R., Xu, W., Su, Z., Yu, Z., Cohn, J., Chae, H., Que, Q., Liu, Z. 2022. CW198 acts as a genetic insulator to block enhancer-promoter interaction in plants. Transgenic Research. https://doi.org/10.1007/s11248-022-00326-6.

An improved procedure for Agrobacterium-mediated transformation of citrus - (Peer Reviewed Journal)
Li, Y., Tang, D., Liu, Z., Chen, J., Cheng, B., Li, Y. 2022. An improved procedure for Agrobacterium-mediated transformation of citrus. Plants. https://doi.org/10.3390/plants11111457.

Meta-analysis of apple (Malus x domestica Borkh.) fruit and juice quality traits for potential use in hard cider production - (Peer Reviewed Journal)
Gottschalk, C.C., Vanderweide, J., Van Nocker, S. 2022. Meta-analysis of apple (Malus x domestica Borkh.) fruit and juice quality traits for potential use in hard cider production. Plants, People, Planet. 3.10262. https://doi.org/10.1002/ppp3.10262.

Notice to fruit growers and nursery growers of release of the pear tree 'Bell' - (Other)

Comparative transcriptomic analysis of apple and peach fruits: insights into fruit type specification. - (Peer Reviewed Journal)
Li, M., Galimba, K.D., Xiao, Y., Dardick, C.D., Mount, S., Callahan, A.M., Liu, Z. 2021. Comparative transcriptomic analysis of apple and peach fruits: insights into fruit type specification. The Plant Journal. 109:1614-1629. https://doi.org/10.1111/tpj.15633.

Polymorphisms and gene expression in the almond IGT family are not correlated to variability in growth habit in major commercial almond cultivars - (Peer Reviewed Journal)

Long term efficacy and safety of RNAi-mediated virus resistance in 'Honeysweet' plum - (Peer Reviewed Journal)
Singh, K., Callahan, A.M., Smith, B., Malinowski, T., Scorza, R., Jarosova, J., Beoni, E., Polak, J., Kundu, J., Dardick, C.D. 2021. Long term efficacy and safety of RNAi-mediated virus resistance in 'Honeysweet' plum. Frontiers in Plant Science. 12:726881. https://doi.org/10.3389/fpls.2021.726881.

Ethylene-mediated modulation of bud phenology, cold hardiness and hormone biosynthesis in peach - (Peer Reviewed Journal)
Liu, J., Islam, T., Sapkota, S., Ravindran, P., Kumar, P., Artlip, T.S., Sherif, S. 2021. Ethephon-mediated modulation of bud phenology, cold hardiness and hormone biosynthesis in peach. Plants. 10(7). https://doi.org/10.3390/plants10071266.

Opportunities and challenges applying gene editing to specialty crops - (Review Article)
Bate, N., Dardick, C.D., De Maagd, R., Williams, R. 2021. Opportunities and challenges applying gene editing to specialty crops. In Vitro Cellular and Developmental Biology - Plants. https://doi.org/10.1007/s11627-021-10208-x.

Robust response to plum pox virus infection via plant biotechnology - (Peer Reviewed Journal)
Ravelonandro, M., Briard, P., Scorza, R., Callahan, A.M., Zagrai, I., Kundu, J., Dardick, C.D. 2021. Robust response to plum pox virus infection via plant biotechnology. Genes. 12(6). https://doi.org/10.3390/genes12060816.

Genetics and genomics of cold hardiness and dormancy in apple - (Book / Chapter)
Liu, J., Artlip, T.S., Sherif, S.M., Wisniewski, M. 2021. Genetics and genomics of cold hardiness and dormancy in apple. Book Chapter. p. 247-270. https://doi.org/10.1007/978-3-030-74682-7_12.

Global analysis of the apple fruit microbiome: are all apples the same - (Peer Reviewed Journal)
Abdelfattah, A., Freilich, S., Bartuv, R., Zhimo, Y., Kumar, A., Biasi, A., Salim, S., Feygenberg, O., Burchard, E.A., Dardick, C.D., Liu, J., Khan, A., Amiri, A., Ellouze, Q., Ali, S., Spadaro, D., Torres, R., Teixido, N., Ozkaya, O., Buehlmann, A., Vero, S., Berg, G., Whitehead, S., Wisniewski, M., Droby, S. 2021. Global analysis of the apple fruit microbiome: are all apples the same. Environmental Microbiology. https://doi.org/10.1111/1462-2920.15469.

Genome-wide changes of regulatory non-coding RNAs reveal pollen development initiated at ecodormancy in peach - (Peer Reviewed Journal)
Yu, J., Bennett Jr, D.R., Dardick, C.D., Zhebentyayeva, T., Abbott, A., Liu, Z., Staton, M. 2021. Genome-wide changes of regulatory non-coding RNAs reveal pollen development initiated at ecodormancy in peach. Frontiers in Plant Science. https://doi.org/10.3389/fmolb.2021.612881.

Fox hunting in wild apples: searching for novel genes in Malus sieversii - (Peer Reviewed Journal)
Wisniewski, M., Artlip, T.S., Liu, J., Ma, J., Burchard, E.A., Norelli, J., Dardick, C.D. 2020. Fox hunting in wild apples: searching for novel genes in Malus sieversii. International Journal of Molecular Sciences. http://dx.doi.org/10.3390/ijms21249516.

The roles of the IGT/LAZY gene family in plant architecture: past, present, and future - (Review Article)
Waite, J.M., Dardick, C.D. 2021. The roles of the IGT/LAZY gene family in plant architecture: past, present, and future. Current Opinion in Plant Biology. 59:101983. https://doi.org/10.1016/j.pbi.2020.101983.

Genetic transformation in peach (Prunus persica L.): challenges and ways forward - (Review Article)
Ricci, A., Sabbadini, S., Prieto, H., Padilla, I.M., Dardick, C.D., Li, Z., Ralph, S., Limera, C., Mezzetti, B., Perez-Jimenez, M., Burgos, L., Petri, C. 2020. Genetic transformation in peach (Prunus persica L.): challenges and ways forward. Plants. 9(8). https://doi.org/10.3390/plants9080971.

Rapid cycling breeding of tree species - (Abstract Only)

Opposing influences of TAC1 and LAZY1 on lateral shoot orientation in Arabidopsis - (Peer Reviewed Journal)
Hollender, C., Hill, J., Waite, J.M., Webb, K.K., Dardick, C.D. 2020. Opposing influences of TAC1 and LAZY1 on lateral shoot orientation in Arabidopsis. Plant Molecular Biology. 10:6051. https://doi.org/10.1038/s41598-020-62962-4.

Identification of early fruit development reference genes in plum - (Peer Reviewed Journal)
Galimba, K.D., Tosetti, R., Loerich, K., Michael, L., Pabhakar, S., Dove, C., Dardick, C.D., Callahan, A.M. 2020. Identification of early fruit development reference genes in plum. PLoS One. https://doi.org/10.1371/journal.pone.0230920.

AtDRO1 is nuclear localized in root tips under native conditions and impacts auxin localization - (Peer Reviewed Journal)
Waite, J.M., Collum, T.D., Dardick, C.D. 2020. AtDRO1 is nuclear localized in root tips under native conditions and impacts auxin localization. Plant Molecular Biology. 103:197-210. https://doi.org/10.1007/s11103-020-00984-2.

Distinctive gene expression patterns define endodormancy to ecodormancy transition in apricot and peach - (Peer Reviewed Journal)
Yu, J., Conrad, A., Decroocq, V., Zhebentyayeva, T., Williams, D., Bennett Jr, D.R., Roch, G., Audergon, J., Dardick, C.D., Liu, Z., Abbott, A., Staton, M. 2020. Distinctive gene expression patterns define endodormancy to ecodormancy transition in apricot and peach. Frontiers in Plant Science. 11:180. https://doi.org/10.3389/fpls.2020.00180.

RNAi-mediated resistance against viruses in perennial fruit plants - (Review Article)
Singh, K., Dardick, C.D., Kundu, J. 2019. RNAi-mediated resistance against viruses in perennial fruit plants. Plants. https://doi.org/10.3390/plants8100359.