Research Project: Enhancement of Apple, Pear, and Sweet Cherry Quality

Location: Physiology and Pathology of Tree Fruits Research

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

Aroma volatiles and sensory quality of organically-grown apple cultivars after dynamic controlled atmosphere (DCA) storage and comparison with CA-stored fruit with and without 1-methylcyclopropene (1-MCP) - (Peer Reviewed Journal)
Al Shoffe, Y., Rudell, D., Park, D., Algul, B.E., Qin, M., Shi, M., Dando, R., Watkins, C.B. 2024. Aroma volatiles and sensory quality of organically-grown apple cultivars after dynamic controlled atmosphere (DCA) storage and comparison with CA-stored fruit with and without 1-methylcyclopropene (1-MCP). Postharvest Biology and Technology. 218. Article 113162. https://doi.org/10.1016/j.postharvbio.2024.113162.

SUNIndx: Visual identification of sun stressed-areas of the fruit using a reflectance index (Sun Index) from hyperspectral images to predict sunscald-risk postharvest on ‘Granny Smith’ apples - (Peer Reviewed Journal)
Mogollon, R., Rudell Jr, D.R., Torres, C. 2024. SUNIndx: Visual identification of sun stressed-areas of the fruit using a reflectance index (Sun Index) from hyperspectral images to predict sunscald-risk postharvest on ‘Granny Smith’ apples. Postharvest Biology and Technology. 27. Article 101828. https://doi.org/10.1016/j.softx.2024.101828.

Excluding sunscald from long-term storage of ‘Granny Smith’ apples - (Peer Reviewed Journal)
Mogollon, R., Mendoza, M., Lorenzo, L., Rudell Jr., D.R., Torres, C. 2024. Excluding sunscald from long-term storage of ‘Granny Smith’ apples. Postharvest Biology and Technology. 216. Article 113044. https://doi.org/10.1016/j.postharvbio.2024.113044.

Effects of Cooling Delay and Harvest Maturity on ‘Gem’ Pear Internal Breakdown Development [abstract] - (Abstract Only)

Rating Pome fruit quality traits using deep learning and image processing - (Pre-print Publication)
Nguyen, N.H., Michaud, J., Mogollon, R., Zhang, H., Hargarten, H.L., Leisso, R.S., Torres, C.A., Honaas, L.A., Ficklin, S. 2024. Rating Pome fruit quality traits using deep learning and image processing. bioRxiv. https://doi.org/10.1101/2024.04.03.588000.

Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica - (Peer Reviewed Journal)
Hadish, J., Hargarten, H.L., Zhang, H., Mattheis, J.P., Honaas, L.A., Ficklin, S.P. 2024. Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica. Postharvest Biology and Technology. 19(3). Article e0297015. https://doi.org/10.1371/journal.pone.0297015. [Corrigendum: PLOS ONE 19(6). Article e0306187. https://doi.org/10.1371/journal.pone.0306187.]

Utilization of perforated zipper-lock packaging bags to improve the quality of stem-on and stem-free ‘Chelan’ and ‘Lapins’ sweet cherries during the storage and marketing periods - (Peer Reviewed Journal)
Zhi, H., Dai, H., Leisso, R.S., Dong, Y. 2023. Utilization of perforated zipper-lock packaging bags to improve the quality of stem-on and stem-free ‘Chelan’ and ‘Lapins’ sweet cherries during the storage and marketing periods. Packaging Technology and Science. 37(3):199-210. https://doi.org/10.1002/pts.2789.

A chromosome-scale assembly for ‘d’Anjou' pear - (Peer Reviewed Journal)
Yocca, A., Akinyuwa, M., Bailey, N., Cliver, B., Estes, H., Guillemette, A., Hasannin, O., Hutchison, J., Jenkins, W., Kaur, I., Khanna, R., Loftin, M., Lopes, L., Moore-Pollard, E., Olofintila, O., Oyebode, G., Patel, J., Thapa, P., Waldinger, M., Zhang, J., Zhang, Q., Goertzen, L., Carey, S., Hargarten, H.L., Mattheis, J., Zhang, H., Jones, T., Boston, L., Grimwood, J., Ficklin, S., Honaas, L.A., Harkess, A. 2024. A chromosome-scale assembly for ‘d’Anjou' pear. G3, Genes/Genomes/Genetics. 14(3). Article jkae003. https://doi.org/10.1093/g3journal/jkae003.

Chilling-related browning of ‘Wonhwang’ pear cortex is associated with the alteration of minerals and metabolism - (Peer Reviewed Journal)
Lwin, H., Torres, C.A., Rudell, D.R., Lee, J. 2023. Chilling-related browning of ‘Wonhwang’ pear cortex is associated with the alteration of minerals and metabolism. Scientia Horticulturae. 321. Article 112321. https://doi.org/10.1016/j.scienta.2023.112321.

Factors affecting development of disorders expressed after storage of ‘Gala’ apple fruit - (Peer Reviewed Journal)
Argenta, L., Wood, R., Mattheis, J.P., Thewes, F., Nesi, C., Neuwald, D. 2023. Factors affecting development of disorders expressed after storage of ‘Gala’ apple fruit. Postharvest Biology and Technology. 204. Article 112439. https://doi.org/10.1016/j.postharvbio.2023.112439.

Metabolic fingerprint of ‘WA 38’ green spot symptoms reveals increased production of epicuticular metabolites by parenchyma - (Peer Reviewed Journal)
Sheick, R., Serra, S., Musacchi, S., Rudell Jr, D.R. 2023. Metabolic fingerprint of ‘WA 38’ green spot symptoms reveals increased production of epicuticular metabolites by parenchyma. Scientia Horticulturae. 321. Article 112257. https://doi.org/10.1016/j.scienta.2023.112257.

Physiological disorders, textural property, and cell wall metabolism of ‘Gem’ pears (Pyrus communis L.) affected by oxygen regimes and harvest maturity under controlled atmosphere storage - (Peer Reviewed Journal)
Dong, Y., Zhi, H., Leisso, R.S. 2023. Physiological disorders, textural property, and cell wall metabolism of ‘Gem’ pears (Pyrus communis L.) affected by oxygen regimes and harvest maturity under controlled atmosphere storage. Scientia Horticulturae. 317:112067. https://doi.org/10.1016/j.scienta.2023.112067.

Pre-storage temperature conditioning reduces cortex browning and cavity and alters organic, amino, and fatty acid metabolism in cold-stored ‘Chuhwangbae’ pears - (Peer Reviewed Journal)
Lwin, H., Leisso, R.S., Lee, J. 2023. Pre-storage temperature conditioning reduces cortex browning and cavity and alters organic, amino, and fatty acid metabolism in cold-stored ‘Chuhwangbae’ pears. Scientia Horticulturae. 315. Article 111989. https://doi.org/10.1016/j.scienta.2023.111989.

PlantTribes2: tools for comparative gene family analysis in plant genomics - (Peer Reviewed Journal)
Wafula, E., Zhang, H., Von Kuster, G., Leebens-Mack, J.H., Honaas, L.A., dePamphilis, C.W. 2023. PlantTribes2: tools for comparative gene family analysis in plant genomics. Frontiers in Plant Science. 13. Article 1011199. https://doi.org/10.3389/fpls.2022.1011199.

Market potential and value-added opportunities of cold-hardy berries and small fruits in the Intermountain West, USA - (Peer Reviewed Journal)
Garg, S., Leisso, R.S., Kim, S., Mayhew, E., Song, M., Jarrett, B., Kuo, W. 2022. Market potential and value-added opportunities of cold-hardy berries and small fruits in the Intermountain West, USA. Journal of Food Science. 88(2):860-876. https://doi.org/10.1111/1750-3841.16426.

Investigations of multiple approaches to reduce green spot incidence in ‘WA 38’ apple - (Peer Reviewed Journal)
Sheick, R., Serra, S., Rudell Jr, D.R., Musacchi, S. 2022. Investigations of multiple approaches to reduce green spot incidence in ‘WA 38’ apple. Agronomy. 12(11). Article 2822. https://doi.org/10.3390/agronomy12112822.

Comparative analysis of metabolic differences between sunburn and sunscald disorder on 'Packham’s triumph’ pear - (Peer Reviewed Journal)
Yoo, J., Sepulveda, G., Rudell Jr, D.R., Torres, C. 2022. Comparative analysis of metabolic differences between sunburn and sunscald disorder on 'Packham’s triumph’ pear. Postharvest Biology and Technology. 195. Article 112153. https://doi.org/10.1016/j.postharvbio.2022.112153.

Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: a case study in Pyrus architecture genes - (Peer Reviewed Journal)
Zhang, H., Wafula, E., Eilers, J.R., Harkess, A., Ralph, P., Timilsena, P., Depamphilis, C., Waite, J.M., Honaas, L.A. 2022. Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: a case study in Pyrus architecture genes. Frontiers in Plant Science. 13. Article 975942. https://doi.org/10.3389/fpls.2022.975942.

A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica) - (Peer Reviewed Journal)
Khan, A., Carey, S., Serrano, A., Zhang, H., Hargarten, H.L., Hale, H., Harkess, A., Honaas, L.A. 2022. A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica). GigaByte. https://doi.org/10.1101/2022.08.24.505160.

1-Methylcyclopropene differentially regulates metabolic responses in the stem-end and calyx-end flesh tissues of 'Empire' apple during long-term controlled atmosphere storage - (Peer Reviewed Journal)
Lee, J., Leisso, R.S., Rudell Jr., D.R., Watkins, C.B. 2022. 1-Methylcyclopropene differentially regulates metabolic responses in the stem-end and calyx-end flesh tissues of 'Empire' apple during long-term controlled atmosphere storage. Postharvest Biology and Technology. 192. Article 112018. https://doi.org/10.1016/j.postharvbio.2022.112018.

Fruit quality of ‘Gala’ and ‘Fuji’ apples cultivated under different environmental conditions - (Peer Reviewed Journal)
Argenta, L.C., do Amarante, C.V., de Freitas, S.T., Brancher, T.L., Nesi, C.N., Mattheis, J.P. 2022. Fruit quality of ‘Gala’ and ‘Fuji’ apples cultivated under different environmental conditions. Scientia Horticulturae. 303. Article 111195. https://doi.org/10.1016/j.scienta.2022.111195.

Monitoring effects of rootstock genotype and soil treatment strategy on postharvest fruit quality in ‘Gala’ apple - (Peer Reviewed Journal)
Hargarten, H.L., Mattheis, J.P., Honaas, L.A. 2022. Monitoring effects of rootstock genotype and soil treatment strategy on postharvest fruit quality in ‘Gala’ apple. HortScience. 57(7):789–798. https://doi.org/10.21273/HORTSCI16407-21.

GEMmaker: Process massive RNA-seq datasets on heterogeneous computational infrastructure - (Peer Reviewed Journal)
Hadish, J., Biggs, T., Shealy, B., Bender, M.R., McKnight, C., Wytko, C., Smith, M., Feltus, A.F., Honaas, L.A., Ficklin, S. 2022. GEMmaker: Process massive RNA-seq datasets on heterogeneous computational infrastructure. BMC Bioinformatics. 23. Article 156. https://doi.org/10.1186/s12859-022-04629-7.

Relationship among dry matter content and maturity indexes at harvest and quality of 'Gala' apples after storage - (Peer Reviewed Journal)
Vieira, M., Argenta, C., Brancher, T.L., de Freitas, S.T., Mattheis, J.P. 2022. Relationship among dry matter content and maturity indexes at harvest and quality of 'Gala' apples after storage. Revista Brasileira de Fruticultura. 44(2). Article e-841. https://doi.org/10.1590/0100-29452022841.

‘d’Anjou’ pear metabolism during ultra-low O2, low CO2 controlled atmosphere storage reflects disorder outcome - (Peer Reviewed Journal)
Mattheis, J.P., Felicetti, D., Rudell Jr, D.R. 2021. ‘d’Anjou’ pear metabolism during ultra-low O2, low CO2 controlled atmosphere storage reflects disorder outcome. Postharvest Biology and Technology. 185. Article 111781. https://doi.org/10.1016/j.postharvbio.2021.111781.

Towards a catalog of pome tree architecture genes: the draft ‘d’Anjou’ genome (Pyrus communis L.) - (Pre-print Publication)
Zhang, H., Wafula, E., Eilers, J.R., Harkess, A., Ralph, P., dePamphilis, C., Waite, J.M., Honaas, L.A. 2021. Towards a catalog of pome tree architecture genes: the draft ‘d’Anjou’ genome (Pyrus communis L.). bioRxiv. https://doi.org/10.1101/2021.11.17.467977.

Persistence of Listeria innocua on fresh apples during long-term controlled atmosphere cold storage with postharvest fungal decay - (Peer Reviewed Journal)
Hamilton, A.M., Ruiz-Llacsahuanga, B., Mendoza, M., Mattheis, J.P., Hanrahan, I., Critzer, F.J. 2021. Persistence of Listeria innocua on fresh apples during long-term controlled atmosphere cold storage with postharvest fungal decay. Journal of Food Protection. 85(1):133–141. https://doi.org/10.4315/JFP-21-232.

Sphingolipids associated with flesh browning onset and development in ‘Cripps Pink’ apples (Malus domestica Borkh.) - (Peer Reviewed Journal)
Sanchez-Contreras, J., Rudell Jr, D.R., Mattheis, J.P., Torres, C.A. 2021. Sphingolipids associated with flesh browning onset and development in ‘Cripps Pink’ apples (Malus domestica Borkh.). Postharvest Biology and Technology. 180. Article 111623. https://doi.org/10.1016/j.postharvbio.2021.111623.

Metabolism and cold chain performance of ‘Chuhwangbae’ Asian pears as impacted by 1-MCP treatment - (Peer Reviewed Journal)
Lwin, H., Rudell Jr, D.R., Lee, J. 2021. Metabolism and cold chain performance of ‘Chuhwangbae’ Asian pears as impacted by 1-MCP treatment. Scientia Horticulturae. 288. Article 110357. https://doi.org/10.1016/j.scienta.2021.110357.

Towards a catalog of pome tree architecture genes: the draft ‘d’Anjou’ genome (Pyrus communis L.) [abstract] - (Abstract Only)
Zhang, H., Eilers, J.R., Honaas, L.A., Waite, J.M. 2021. Towards a catalog of pome tree architecture genes: the draft ‘d’Anjou’ genome (Pyrus communis L.) [abstract]. American Society of Horticulture Science Meeting. 56(9):S55.

Growing condition and storage regime effects on fruit quality and physiological disorders on ‘Honeycrisp’ apples [abstract] - (Abstract Only)
Galeni, M., Mattheis, J.P., Torres, C. 2021. Growing condition and storage regime effects on fruit quality and physiological disorders on ‘Honeycrisp’ apples [abstract]. American Society of Horticulture Science Meeting. Paper No. 35141.

Distinguishing the metabolic fingerprints of carbon dioxide apple storage disorders from other disorders [abstract] - (Abstract Only)
McTavish, C.K., Milne, S.M., Tudor, E., Celebrezze, J., Hanrahan, I., Mattheis, J.P., Rudell Jr, D.R. 2021. Distinguishing the metabolic fingerprints of carbon dioxide apple storage disorders from other disorders [abstract]. American Society of Horticulture Science Meeting. Paper No. 39019.

Comparative analysis of metabolomic differences between the sunburn and sunscald disorder on 'Packham’s triumph’ pear [abstract] - (Abstract Only)
Yoo, J., Rudell Jr, D.R., Torres, C. 2021. Comparative analysis of metabolomic differences between the sunburn and sunscald disorder on 'Packham’s triumph’ pear [abstract]. American Society of Horticulture Science Meeting. Paper No. 35625.

Triggering and eliminating sun-related apple peel browning occurring during cold storage using heat [abstract] - (Abstract Only)
McTavish, C.K., Valdez, E.L., Tudor, E.M., Torres, C., Mattheis, J.P., Rudell Jr, D.R. 2021. Triggering and eliminating sun-related apple peel browning occurring during cold storage using heat [abstract]. American Society of Horticulture Science Meeting. Paper No. 35963.

Detection of non-visible sun stress in ‘Granny Smith’ apples using hyperspectral imaging [abstract] - (Abstract Only)
Mogollon, R., Torres, C., Rudell Jr, D.R. 2021. Detection of non-visible sun stress in ‘Granny Smith’ apples using hyperspectral imaging [abstract]. American Society of Horticulture Science Meeting. Paper No. 35134.

Transcriptomics of differential ripening in ‘d’Anjou pear (Pyrus communis L.) - (Peer Reviewed Journal)
Honaas, L.A., Hargarten, H.L., Hadish, J., Ficklin, S., Serra, S., Musacchi, S., Wafula, E., Mattheis, J.P., dePamphilis, C., Rudell Jr, D.R. 2021. Transcriptomics of differential ripening in ‘d’Anjou pear (Pyrus communis L.). Frontiers in Plant Science. 12. Article 609684. https://doi.org/10.3389/fpls.2021.609684.

Characterization and quantification of postharvest losses of apple fruit stored under commercial conditions - (Peer Reviewed Journal)
Argenta, L.C., de Freitas, S.T., Mattheis, J.P., Vieira, M.J., Ogoshi, C. 2021. Characterization and quantification of postharvest losses of apple fruit stored under commercial conditions. HortScience. 56(5):608-616. https://doi.org/10.21273/HORTSCI15771-21.

Characterization of the relationship between postharvest fungal rot and Listeria innocua die-off rates on Gala apples during long-term storage [Abstract] - (Abstract Only)
Hamilton, A., Ruiz, B., Mendoza, M., Mattheis, J.P., Hanrahan, I., Critzer, F. 2021. Characterization of the relationship between postharvest fungal rot and Listeria innocua die-off rates on Gala apples during long-term storage [Abstract]. International Association for Food Protection. 84(5):49.

‘Honeycrisp’ apple (Malus domestica Borkh.) fruit response to controlled atmosphere storage with the low oxygen limit established by monitoring chlorophyll fluorescence - (Peer Reviewed Journal)
Mattheis, J.P., Rudell Jr, D.R. 2020. ‘Honeycrisp’ apple (Malus domestica Borkh.) fruit response to controlled atmosphere storage with the low oxygen limit established by monitoring chlorophyll fluorescence. HortScience. 56(2):173-176. https://doi.org/10.21273/HORTSCI15404-20.