Research Project: Developmental Genomics and Metabolomics Influencing Temperate Tree Fruit Quality

Location: Physiology and Pathology of Tree Fruits Research

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

Metabolic adaptation of apple and pear peel during transitions in the postharvest environment [abstract] - (Abstract Only)
Rudell Jr, D.R. 2020. Metabolic adaptation of apple and pear peel during transitions in the postharvest environment [abstract]. American Chemical Society Abstracts. AGFD 110.

Characterization of carbon dioxide-related storage disorder symptoms across multiple apple cultivars [abstract] - (Abstract Only)
McTavish, C.K., Tudor, E.M., Celebrezze, J., Mattheis, J.P., Rudell Jr, D.R., Hanrahan, I. 2020. Characterization of carbon dioxide-related storage disorder symptoms across multiple apple cultivars [abstract]. American Society of Horticulture Science Meeting. Paper No. 33564.

A convergence of sunlight and cold chain: The influence of sun exposure on postharvest apple peel metabolism - (Peer Reviewed Journal)
McTavish, C.K., Poirier, B.C., Torres, C.A., Mattheis, J.P., Rudell Jr, D.R. 2020. A convergence of sunlight and cold chain: The influence of sun exposure on postharvest apple peel metabolism. Postharvest Biology and Technology. 164. Article 111164. https://doi.org/10.1016/j.postharvbio.2020.111164.

Integrating functional genomics and classic postharvest managment [abstract] - (Abstract Only)
Hargarten, H.L., Honaas, L.A. 2021. Integrating functional genomics and classic postharvest managment [abstract]. International Symposium on Integrating Canopy, Rootstock and Environmental. p.75.

Genomics approaches for postharvest enhancement of Rosaceous tree fruit [abstract] - (Abstract Only)
Honaas, L.A., Hargarten, H.L., Hadish, J., Ficklin, S., Wafula, E., Mattheis, J.P., Rudell Jr, D.R., dePamphilis, C. 2020. Genomics approaches for postharvest enhancement of Rosaceous tree fruit [abstract]. Genomics of the Rosaceae. p. 8.

Storage environment impacts on ‘Honeycrisp’ apple volatile production [abstract] - (Abstract Only)

Functional genomics of postharvest physiology in pome fruits - (Abstract Only)
Honaas, L.A., Hargarten, H.L., Hadish, J., Ficklin, S., Wafula, E., Mattheis, J.P., Rudell Jr, D.R., Depamphilis, C. 2020. Functional genomics of postharvest physiology in pome fruits. Annual International Plant & Animal Genome Conference. W467.

SHR4z, a novel decoy effector from the haustorium of the parasitic weed Striga gesnerioides, suppresses host plant immunity - (Peer Reviewed Journal)
Su, C., Lui, H., Wafula, E., Honaas, L.A., dePamphilis, C., Timdo, M. 2019. SHR4z, a novel decoy effector from the haustorium of the parasitic weed Striga gesnerioides, suppresses host plant immunity. New Phytologist. 226:641-643. https://doi.org/10.1111/nph.16351.

Extending ‘Granny Smith’ apple superficial scald control following long-term ultra-low oxygen controlled atmosphere storage - (Peer Reviewed Journal)
Poirier, B.C., Mattheis, J.P., Rudell Jr, D.R. 2019. Extending ‘Granny Smith’ apple superficial scald control following long-term ultra-low oxygen controlled atmosphere storage. Postharvest Biology and Technology. 161. Article 111062. https://doi.org/10.1016/j.postharvbio.2019.111062.

Genome sequence of Striga asiatica provides insight into the evolution of plant parasitism - (Peer Reviewed Journal)
Yoshida, S., Kim, S., Wafula, E., Tanskanen, J., Kim, Y., Honaas, L.A., Yang, Z., Spallek, T., Conn, C., Ichihashi, Y., Cheong, K., Cui, S., Der, J., Gundlach, H., Jiao, Y., Hori, C., Ishida, J.K., Kasahara, H., Takatoshi, K., Kim, M., Koo, N., Laohavisit, A., Lee, Y., Lumba, S., McCourt, P., Mortimer, J.C., Musembi Mutuku, J., Nomura, T., Sasaki-Sekimoto, Y., Seto, Y., Wang, Y., Wakatake, T., Sakakibara, H., Demura, T., Yamaguchi, S., Yoneyama, K., Manabe, R., Nelson, D.C., Schulman, A.H., Timko, M.P., dePamphilis, C.W., Choi, D., Shirasu, K. 2019. Genome sequence of Striga asiatica provides insight into the evolution of plant parasitism. Current Biology. 29(18):3041-3052.e4. https://doi.org/10.1016/j.cub.2019.07.086.

‘Fuji’ and ‘Gala’ apple fruit responses to controlled atmosphere established during temperature conditioning after harvest - (Abstract Only)
Mattheis, J.P. 2019. ‘Fuji’ and ‘Gala’ apple fruit responses to controlled atmosphere established during temperature conditioning after harvest. American Society of Horticulture Science Meeting. Paper No 30416.

Risk versus reward: host dependent parasite mortality rates and phenotypes in the facultative generalist Triphysaria versicolor - (Peer Reviewed Journal)
Honaas, L.A., Jones, S., Farell, N., Kamerow, W., Zhang, H., Vescio, K., Altman, N., Yoder, J., dePamphilis, C. 2019. Risk versus reward: host dependent parasite mortality rates and phenotypes in the facultative generalist Triphysaria versicolor. Biomed Central (BMC) Plant Biology. Article 334. https://doi.org/10.1186/s12870-019-1856-1.

Responses of ‘Honeycrisp’ apples to short-term controlled atmosphere storage established during temperature conditioning - (Peer Reviewed Journal)
Serban, C., Kalcsits, L., DeEll, J., Mattheis, J.P. 2019. Responses of ‘Honeycrisp’ apples to short-term controlled atmosphere storage established during temperature conditioning. HortScience. 54(9):1532-1539. https://doi.org/10.21273/HORTSCI14182-19.

PlantTribes: Galaxy tools for comparative gene family analysis in plant genomics [abstract] - (Abstract Only)
Wafula, E., Von Kuster, G., Der, J.P., Honaas, L.A., Ayyampalayam, S., Wickett, N., Leebens-Mack, J., dePamphillis, C. 2019. PlantTribes: Galaxy tools for comparative gene family analysis in plant genomics [abstract]. Plant and Animal Genome Conference. p. 12.

Cross cultivar RNA-seq: challenges and perspectives - (Abstract Only)
Honaas, L.A., Wafula, E., Simenc, M., Der, J.P., Hargarten, H.L., Hadish, J., Depamphilis, C., Ficklin, S. 2019. Cross cultivar RNA-seq: challenges and perspectives. American Society of Horticulture Science Meeting. Meeting Abstract.

Application of workflow designed to leverage transcriptome data for enhanced gene expression analysis in tree fruits - (Abstract Only)
Hargarten, H.L., Schmidt, R., Kahan, E., Honaas, L.A. 2019. Application of workflow designed to leverage transcriptome data for enhanced gene expression analysis in tree fruits. American Society of Horticulture Science Meeting. Meeting Abstract.

Apple fruit cutin composition during storage is altered by sunlight exposure in the orchard [abstract] - (Abstract Only)
Rudell Jr, D.R., Poirier, B.C., Honaas, L.A., McTavish, C.K., Torres, C., Mattheis, J.P. 2019. Apple fruit cutin composition during storage is altered by sunlight exposure in the orchard [abstract]. American Society of Horticulture Science Meeting. 53(9):S130.

Transcriptomics of host-specific interactions in natural populations of the parasitic plant purple witchweed (Striga hermonthica) - (Peer Reviewed Journal)
Lopes, L., Bellis, E., Wafula, E., Hearne, S., Honaas, L.A., Ralph, P., Unachukwu, N., dePamphilis, C., Lasky, J. 2019. Transcriptomics of host-specific interactions in natural populations of the parasitic plant purple witchweed (Striga hermonthica). Weed Science. 67(4):397-411. https://doi.org/10.1017/wsc.2019.20.

Fruit canopy positioning affects fruit calcium and potassium concentrations, disorder incidence, and fruit quality for ‘Honeycrisp’ apple - (Peer Reviewed Journal)
Kalcsits, L., Mattheis, J.P., Giordani, L., Reid, M., Mullin, K. 2019. Fruit canopy positioning affects fruit calcium and potassium concentrations, disorder incidence, and fruit quality for ‘Honeycrisp’ apple. Canadian Journal of Plant Science. 99(5): 761-771. https://doi.org/10.1139/cjps-2019-0017.

Apple fruit responses to controlled atmosphere established during postharvest temperature conditioning - (Abstract Only)
Mattheis, J.P. 2020. Apple fruit responses to controlled atmosphere established during postharvest temperature conditioning. HortScience. 54(9S):S129. https://doi.org/10.21273/HORTSCI.54.9S.S1.

Assessing preharvest field temperature and at-harvest fruit quality for prediction of soft scald risk of 'Honeycrisp' apple fruit during cold storage - (Peer Reviewed Journal)
Leisso, R., Hanrahan, I., Mattheis, J.P. 2019. Assessing preharvest field temperature and at-harvest fruit quality for prediction of soft scald risk of 'Honeycrisp' apple fruit during cold storage. HortScience. 54(5):910–915. https://doi.org/10.21273/HORTSCI13558-18.

Co-expression networks provide insight into postharvest fruit physiology - (Abstract Only)
Honaas, L.A., Hargarten, H.L., Ficklin, S., Hadish, J., Wafula, E., Depamphilis, C., Mattheis, J.P., Rudell Jr, D.R. 2019. Co-expression networks provide insight into postharvest fruit physiology. Plant and Animal Genome Conference. Paper No. PE0664.

Application of workflow designed to leverage transcriptome data for enhanced gene expression analysis in tree fruits - (Abstract Only)
Hargarten, H.L., Schmidt, R., Kahn, E., Honaas, L.A. 2019. Application of workflow designed to leverage transcriptome data for enhanced gene expression analysis in tree fruits. Plant and Animal Genome Conference. Meeting Abstract.

Antioxidant metabolism in stem and calyx end tissues in relation to flesh browning development during storage of 1-methylcyclopropene treated ‘Empire’ apples - (Peer Reviewed Journal)
Lee, J., Cheng, L., Rudell Jr, D.R., Nock, J.F., Watkins, C.B. 2019. Antioxidant metabolism in stem and calyx end tissues in relation to flesh browning development during storage of 1-methylcyclopropene treated ‘Empire’ apples. Postharvest Biology and Technology. 149:66-73. https://doi.org/10.1016/j.postharvbio.2018.11.015.

Canopy attachment position influences metabolism and peel constituency of European pear fruit - (Peer Reviewed Journal)
Serra, S., Sullivan, N., Mattheis, J.P., Musacchi, S., Rudell Jr, D.R. 2018. Canopy attachment position influences metabolism and peel constituency of European pear fruit. Biomed Central (BMC) Plant Biology. 18:364. https://doi.org/10.1186/s12870-018-1544-6.

Co-expression networks provide insights into molecular mechanisms of postharvest temperature modulation of apple fruit to reduce superficial scald - (Peer Reviewed Journal)
Honaas, L.A., Hargarten, H.L., Ficklin, S., Hadish, J., Wafula, E., dePamphilis, C., Mattheis, J.P., Rudell Jr, D.R. 2019. Co-expression networks provide insights into molecular mechanisms of postharvest temperature modulation of apple fruit to reduce superficial scald. Postharvest Biology and Technology. 149:27-41. https://doi.org/10.1016/j.postharvbio.2018.09.016.

High storage humidity affects fruit quality attributes and incidence of fruit cracking in cold-stored ‘Royal Gala’ apples - (Peer Reviewed Journal)
Lee, J., Mattheis, J.P., Rudell Jr, D.R. 2019. High storage humidity affects fruit quality attributes and incidence of fruit cracking in cold-stored ‘Royal Gala’ apples. HortScience. 54(1):149-154. https://doi.org/10.21273/HORTSCI13406-18.

Leveraging transcriptome data for enhanced gene expression analysis in apple - (Peer Reviewed Journal)
Hargarten, H.L., Waliullah, S., Kalcsits, L., Honaas, L.A. 2018. Leveraging transcriptome data for enhanced gene expression analysis in apple. Journal of the American Society for Horticultural Science. 143(5):333-346. https://doi.org/10.21273/JASHS04424-18.

Functional genomics of `D´Anjou' pear fruit quality and maturity [abstract] - (Abstract Only)
Honaas, L.A., Wafula, E., dePamphilis, C., Serra, S., Musacchi, S. 2018. Functional genomics of `D´Anjou' pear fruit quality and maturity [abstract]. International Society of Horticultural Science Proceedings. p. 26.

Enhancing postharvest tree fruit quality with functional genomics - (Abstract Only)
Honaas, L.A., Hargarten, H.L., Ficklin, S., Hadish, J., Wafula, E., Depamphilis, C., Mattheis, J.P., Rudell Jr, D.R. 2018. Enhancing postharvest tree fruit quality with functional genomics. American Society of Horticulture Science Meeting. Paper No. 28404.

Alterations in peel secondary metabolism are associated with superficial scald in apples - (Abstract Only)
Poirier, B.C., Buchanan, D.A., Rudell Jr, D.R., Mattheis, J.P. 2018. Alterations in peel secondary metabolism are associated with superficial scald in apples. American Society of Horticulture Science Meeting. Paper No. 29052.

Influence of tree position on free non-polar cuticular metabolites of ‘d’Anjou’ pear during controlled atmosphere storage - (Abstract Only)
Rudell Jr, D.R., Musacchi, S., Serra, S., Mattheis, J.P. 2018. Influence of tree position on free non-polar cuticular metabolites of ‘d’Anjou’ pear during controlled atmosphere storage. American Society of Horticulture Science Meeting. Paper No. 29379.

Utilizing nontargeted metabolomics to characterize delayed sunscald development on apple - (Abstract Only)
Mctavish, C.K., Sullivan, N., Torres, C., Mattheis, J.P., Rudell Jr, D.R. 2018. Utilizing nontargeted metabolomics to characterize delayed sunscald development on apple. American Society of Horticulture Science Meeting. Paper No. 28727.

IAD value at harvest as a predictor for ‘Anjou’ fruit storage performance [abstract] - (Abstract Only)

Apple - (Book / Chapter)
Watkins, C.B., Mattheis, J.P. 2019. Apple. In: Tonetto de Freitas, S., Pareek S., editors. Postharvest Physiological Disorders in Fruits and Vegetables, 1st Edition. Boca Raton, Florida: Taylor & Francis Group, CRC Press. p. 165-207. https://doi.org/10.1201/b22001.

Relationship between dry matter content at harvest and maturity index and post-harvest quality of "Fuji" apples - (Peer Reviewed Journal)
Vieria, M., Argenta, L., Mattheis, J.P. 2018. Relationship between dry matter content at harvest and maturity index and post-harvest quality of "Fuji" apples. Revista Brasileira de Fruticultura. 40:e-596. http://dx.doi.org/10.1590/0100-29452018596.

Superficial scald risk assessment assay for apples - (Experiment Station)
Blakey, R., Rudell Jr, D.R. 2018. Superficial scald risk assessment assay for apples. WSU Extension Bulletin. Paper No. FS287E.

Differential partitioning of triterpenes and triterpene esters in apple peel - (Peer Reviewed Journal)
Poirier, B.C., Buchanan, D.A., Rudell Jr, D.R., Mattheis, J.P. 2018. Differential partitioning of triterpenes and triterpene esters in apple peel. Journal of Agricultural and Food Chemistry. https://doi.org/10.1021/acs.jafc.7b04509.

Metabolic profiling variations within D’Anjou pear fruit from different canopy positions - (Peer Reviewed Journal)
Rudell Jr, D.R., Sullivan, N.L., Mattheis, J.P., Musacchi, S. 2017. Metabolic profiling variations within D’Anjou pear fruit from different canopy positions. HortScience. 52(11):1501–1510. https://doi.org/10.21273/HORTSCI12375-17.

Enhancing postharvest tree fruit quality with functional genomics - (Abstract Only)
Honaas, L.A., Hargarten, H.L., Der, J., Wafula, E., Depamphilis, C., Rudell Jr, D.R., Mattheis, J.P. 2018. Enhancing postharvest tree fruit quality with functional genomics. Plant and Animal Genome Conference. January 12, 2018, San Diego, California.

Leveraging public transcriptome data for enhanced qPCR probe design - (Abstract Only)
Waliullah, S., Honaas, L.A., Kalcsits, L.A. 2018. Leveraging public transcriptome data for enhanced qPCR probe design. Plant and Animal Genome Conference. January 12, 2018, San Diego, California.

“Stealth dissemination” of macrophage-tumor cell fusions cultured from blood of patients with pancreatic ductal adenocarcinoma - (Peer Reviewed Journal)
Clawson, G., Matters, G., Xin, P., McGovern, C., Wafula, E., dePamphilis, C., Meckley, M., Wong, J., Eckert, K., Stewart, L., D'Jamoos, C., Altman, N., Kawsawa, Y., Du, Z., Honaas, L.A., Abraham, T. 2017. “Stealth dissemination” of macrophage-tumor cell fusions cultured from blood of patients with pancreatic ductal adenocarcinoma. PLoS ONE. 12(9):e0184451. https://doi.org/10.1371/journal.pone.0184451.

Controlled atmosphere pO2 alters ripening dynamics of 1-MCP treated ‘d’Anjou’ pear (Pyrus communis L.) fruit - (Peer Reviewed Journal)
Mattheis, J.P. 2017. Controlled atmosphere pO2 alters ripening dynamics of 1-MCP treated ‘d’Anjou’ pear (Pyrus communis L.) fruit. HortScience. 52(10):1385–1389. https://doi.org/10.21273/HORTSCI12286-17.

Metabolism characterizing sun exposed and shaded side peel of four apple cultivars during cold storage - (Proceedings)
Mctavish, C.K., Torres, C., Mattheis, J.P., Rudell Jr, D.R. 2017. Metabolism characterizing sun exposed and shaded side peel of four apple cultivars during cold storage. Postharvest Unlimited. October 17, 2017, Madrid, Sprain.

A practical examination of RNA isolation methods for European pear (Pyrus communis) - (Peer Reviewed Journal)
Honaas, L.A., Kahn, E.M. 2017. A practical examination of RNA isolation methods for European pear (Pyrus communis). BMC Research Notes. doi: 10.1186/s13104-017-2564-2.

‘Golden Delicious’ and ‘Honeycrisp’ apple response to controlled atmosphere storage with oxygen set point determined in response to fruit chlorophyll fluorescence - (Abstract Only)
Mattheis, J.P. 2017. ‘Golden Delicious’ and ‘Honeycrisp’ apple response to controlled atmosphere storage with oxygen set point determined in response to fruit chlorophyll fluorescence. HortScience. 52(9)(Suppl.), S180.

Enhancing postharvest tree fruit quality with functional genomics [abstract] - (Abstract Only)
Honaas, L.A. 2017. Enhancing postharvest tree fruit quality with functional genomics [abstract]. HortScience. 52(9):S252.

Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis - (Peer Reviewed Journal)
Gapper, N.E., Hertog, M., Lee, J., Buchanan, D.A., Leisso, R.S., Giovannoni, J.J., Johnston, J.W., Shaffer, R.J., Micolai, B.M., Mattheis, J.P., Watkins, C.B., Rudell Jr, D.R. 2017. Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis. Biomed Central (BMC) Plant Biology. 17:77. https://doi.org/10.1186/s12870-017-1030-6.

Controlled atmosphere storage, temperature conditioning, and antioxidant treatment alter postharvest 'Honeycrisp' metabolism - (Peer Reviewed Journal)
Leisso, R.S., Mattheis, J.P., Rudell, D.R. 2017. Controlled atmosphere storage, temperature conditioning, and antioxidant treatment alter postharvest 'Honeycrisp' metabolism. HortScience. 52(3):423–431. doi:10.21273/HORTSCI11436-16.

Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome [abstract] - (Abstract Only)
Honaas, L.A., Wafula, E.K., Wickett, N.J., Der, J.P., Zhang, Y., Edger, P.P., Altman, N.S., Pires, C., Leebens-Mack, J.H., dePamphilis, C.W. 2016. Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome [abstract]. Plant and Animal Genome Conference. p. 12.

Impacts of 1-Methylcyclopropene and controlled atmosphere established during conditioning on development of bitter pit in ‘Honeycrisp’ apples - (Peer Reviewed Journal)
Mattheis, J.P., Rudell, D.R., Hanrahan, I. 2017. Impacts of 1-Methylcyclopropene and controlled atmosphere established during conditioning on development of bitter pit in ‘Honeycrisp’ apples. HortScience. 52:132-137. doi:10.21273/HoRTSCI11368-16.

Antioxidant metabolism and gene expression during ‘‘stain’’ development on ‘Fuji’ apples during cold storage - (Peer Reviewed Journal)
Torres, C.A., Hernandez, O., Myoa-León, M.A., Razmilic, I., Rudell Jr, D.R. 2016. Antioxidant metabolism and gene expression during ‘‘stain’’ development on ‘Fuji’ apples during cold storage. HortScience. 51(8):1031–1037.

Fruit position within pear trees impacts ripening and associated metabolism after harvest [abstract] - (Abstract Only)
Rudell Jr, D.R., Serra, S., Sullivan, N.L., Mattheis, J.P., Musacchi, S. 2016. Fruit position within pear trees impacts ripening and associated metabolism after harvest [abstract]. Metabolomics. 2054:76.

Evaluating fruit quality and maturity consistency in large open vase trained ‘D’Anjou’ trees - (Abstract Only)
Serra, S., Rudell Jr, D.R., Mattheis, J.P., Musacchi, S. 2016. Evaluating fruit quality and maturity consistency in large open vase trained ‘D’Anjou’ trees. Annual Meeting Horticultural Society. Available: https://ashs.confex.com/ashs/2016/meetingapp.cgi/Paper/24080.

Fall and summer pruning to control vigor in d'Anjou pear - (Abstract Only)
Musacchi, S., Serra, S., Mattheis, J.P. 2016. Fall and summer pruning to control vigor in d'Anjou pear. International Symposium on Integrating Canopy, Rootstock and Environmental. p. 30.

Ex ante economic evaluation of technologies for managing postharvest physiological disorders - (Peer Reviewed Journal)
Rickard, B.J., Rudell Jr, D.R., Watkins, C.B. 2016. Ex ante economic evaluation of technologies for managing postharvest physiological disorders. HortScience. 51(5):537-542.

Apple fruit responses following exposure to nitric oxide - (Abstract Only)
Mattheis, J.P., Rudell Jr, D.R. 2016. Apple fruit responses following exposure to nitric oxide. International Society for Horticultural Science Meeting. N/A.

Storage temperature and 1-MCP treatment affect storage disorders and physiological attributes of ‘Royal Gala’ apples - (Peer Reviewed Journal)
Lee, J., Mattheis, J.P., Rudell Jr, D.R. 2016. Storage temperature and 1-MCP treatment affect storage disorders and physiological attributes of ‘Royal Gala’ apples. HortScience. 51:84-93.

Managing ‘Bartlett’ pear fruit ripening with 1-methylcyclopropene reapplication during cold storage - (Peer Reviewed Journal)
Argenta, L.C., Mattheis, J.P., Fan, X., Amarante, C.V. 2016. Managing ‘Bartlett’ pear fruit ripening with 1-methylcyclopropene reapplication during cold storage. Postharvest Biology and Technology. 113:125-130.

Prediction and diagnosis of apple fruit physiological disorders - (Abstract Only)
Mattheis, J.P., Rudell Jr, D.R., Leisso, R. 2015. Prediction and diagnosis of apple fruit physiological disorders. Meeting Abstract. N/A.

Effect of 1-Methylcyclopropene coupled with controlled atmosphere storage on the ripening and quality of ‘Cavendish’ bananas - (Abstract Only)
Suryanungsih, L., Mattheis, J.P. 2015. Effect of 1-Methylcyclopropene coupled with controlled atmosphere storage on the ripening and quality of ‘Cavendish’ bananas. Meeting Abstract. N/A.