Publications
Plant Physiology • Adaptation • Dormancy • Genomics • Epigenomics
The research conducted in this group is wide in scope. We have a programmatic belief that plant physiology and genetics are intertwined, and that many exciting questions in plant adaptation can be answered by investigating the interface.
Student / postdoc led
🍇 Grapevine
🍎 Apple
🌼 Brassica / canola
🌾 Rice
Genetics / genomics
Phenotyping
Cold / winter
Modeling
Wang H., Londo J.P. (2026). Chilling Accumulation Shapes Transcriptomic Responses to Warming Exposure During Grapevine Deacclimation. Physiologia Plantarum 178(4).
Campos‐Arguedas F., Kirchhof E., North M.G., Londo J.P., Bates T., van Leeuwen C., Destrac‐Irvine A., Bois B., Kovaleski A.P. (2026). Cold hardiness dynamics predict budbreak and associated low‐temperature threats in grapevine. New Phytologist 250(4), 2203-2220.
Migicovsky Z., Elzinga C., Lauzon M.C., Connor T., DeViller K., Dinn C., Earle G.M., Hockley E., Lennon O., Ricker L.A., Roberts P.M., Robinson K.M., Sharma A., Spencer P.N., Stockdale S., Tingley L.L., Yates A., Londo J.P., Cousins P. (2025). Genomic structure and ex situ conservation of the North American grapevine Vitis labrusca. PLANTS, PEOPLE, PLANET 8(5), 1649-1661.
Sharma P., Alahakoon D., Londo J.P., Fennell A. (2025). Genetic regulation of leaf morphology in own-rooted and grafted vines of an F1 rootstock population. Frontiers in Plant Science 16.
Wang H., Londo J.P. (2025). VineColD: an integrative database for global historical tracing and real-time monitoring of grapevine cold hardiness. Database 2025.
Massonnet M., Cochetel N., Ricciardi V., Minio A., Figueroa-Balderas R., Londo J.P., Cantu D. (2025). Evolutionary conservation of the grape sex-determining region in angiosperms and emergence of dioecy in Vitaceae. Nature Communications 16(1).
Wang H., Pan Y., Londo J.P. (2025). Tetralone-ABA enhances winter cold acclimation, reduces deacclimation, and delays budbreak in V. vinifera and V. hybrid grapevines. Plant Stress 16, 100861.
Londo J.P., Kovaleski A.P. (2025). Integrating cold hardiness and deacclimation resistance demonstrates a conserved response to chilling accumulation in grapevines. Journal of Experimental Botany 76(11), 3158-3171.
Wang H., Kovaleski A.P., Londo J.P. (2024). Physiological and transcriptomic characterization of cold acclimation in endodormant grapevine under different temperature regimes. Physiologia Plantarum 176(6).
Wang H., Moghe G.D., Kovaleski A.P., Keller M., Martinson T.E., Wright A.H., Franklin J.L., Hébert-Haché A., Provost C., Reinke M., Atucha A., North M.G., Russo J.P., Helwi P., Centinari M., Londo J.P. (2023). NYUS.2: an automated machine learning prediction model for the large-scale real-time simulation of grapevine freezing tolerance in North America. Horticulture Research 11(2).
Strickland D.A., Londo J.P., Cox K.D. (2024). Comparison of Standard Calendar GA4+7 Plant Growth Regulator Programs to Applications Timed to Rainfall Events for Management of Scarf Skin, a Fruit Finish Disorder of Apple. PhytoFrontiers™ 4(2), 141-149.
Cochetel N., Minio A., Guarracino A., Garcia J.F., Figueroa-Balderas R., Massonnet M., Kasuga T., Londo J.P., Garrison E., Gaut B.S., Cantu D. (2023). A super-pangenome of the North American wild grape species. Genome Biology 24(1).
de Sousa Moreira L., Clark M.D., Tabb A., Karn A., Londo J.P., Zou C., Sun Q., van Zyl S., Prins B., DeLong J.D., Burhans A., Yang H.C., Naegele R.P. (2024). Identification of Novel Quantitative Trait Loci Associated with Table Grape Fruit Quality Characteristics in a Segregating Population and Transferability of Existing Quality Markers. J. Amer. Soc. Hort. Sci. 149(1), 50-60.
Reisch B.I., Cadle-Davidson L., Ugochukwu I., Gavin S., Londo J.P., Martinson T.E. (2023). Contributions of the VitisGen2 project to grapevine breeding and genetics. Vitis 62, 88-91.
Patel S., Harris Z.N., Londo J.P., Miller A., Fennell A. (2023). Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’. Gigabyte 2023, 1-18.
Harris Z.N., Pratt J.E., Kovacs L.G., Klein L.L., Kwasniewski M.T., Londo J.P., Wu A.S., Miller A.J. (2023). Grapevine scion gene expression is driven by rootstock and environment interaction. BMC Plant Biology 23(1).
Kovaleski A.P., North M.G., Martinson T.E., Londo J.P. (2023). Development of a new cold hardiness prediction model for grapevine using phased integration of acclimation and deacclimation responses. Agricultural and Forest Meteorology 331, 109324.
Alzohairy S.A., Londo J.P., Heinitz C., Naegele R.P. (2023). Cultivar and Maternal Plant Environment Influence Cold Stratification Requirements and Germination Rates of Vitis Species. HortScience 58(5), 515-524.
Londo J.P., Moyer M.M., Mireles M., Mills L., Keller M., Workmaster B.A., Atucha A., Kovaleski A.P. (2022). Evaluation of Sample Preparation Practices Common with Differential Thermal Analysis of Grapevine Bud Cold Hardiness. American Journal of Enology and Viticulture 74(1), 0740002.
Islam M.T., Kudla-Williams C., Kar S., Londo J.P., Centinari M., Rosa C. (2022). Deciphering genome-wide transcriptomic changes in grapevines heavily infested by spotted lanternflies. Frontiers in Insect Science 2.
Brillouet J.M., Romieu C., Bacilieri R., Nick P., Trias-Blasi A., Maul E., Solymosi K., Teszlák P., Jiang J.F., Sun L., Ortolani D., Londo J.P., Gutierrez B., Prins B., Reynders M., Van Caekenberghe F., Maghradze D., Marchal C., Sultan A., Thomas J.F., Scherberich D., Fulcrand H., Roumeas L., Billerach G., Salimov V., Musayev M., Ejaz Ul Islam Dar M., Peltier J.B., Grisoni M. (2022). Tannin phenotyping of the Vitaceae reveals a phylogenetic linkage of epigallocatechin in berries and leaves. Annals of Botany 130(2), 159-171.
Alahakoon D., Fennell A., Helget Z., Bates T., Karn A., Manns D., Mansfield A.K., Reisch B.I., Sacks G., Sun Q., Zou C., Cadle-Davidson L., Londo J.P. (2022). Berry Anthocyanin, Acid, and Volatile Trait Analyses in a Grapevine-Interspecific F2 Population Using an Integrated GBS and rhAmpSeq Genetic Map. Plants 11(5), 696.
Yin L., Karn A., Cadle-Davidson L., Zou C., Londo J., Sun Q., Clark M.D. (2022). Candidate resistance genes to foliar phylloxera identified at Rdv3 of hybrid grape. Horticulture Research 9.
Wang H., Dami I.E., Martens H., Londo J.P. (2022). Transcriptomic analysis of grapevine in response to ABA application reveals its diverse regulations during cold acclimation and deacclimation. Fruit Research 2(1), 1-12.
Harris Z.N., Awale M., Bhakta N., Chitwood D.H., Fennell A., Frawley E., Klein L.L., Kovacs L.G., Kwasniewski M., Londo J.P., Ma Q., Migicovsky Z., Swift J.F., Miller A.J. (2021). Multi-dimensional leaf phenotypes reflect root system genotype in grafted grapevine over the growing season. GigaScience 10(12).
Gutierrez B., Schwaninger H., Meakem V., Londo J., Zhong G.Y. (2021). Phenological diversity in wild and hybrid grapes (Vitis) from the USDA-ARS cold-hardy grape collection. Scientific Reports 11(1).
Zou C., Massonnet M., Minio A., Patel S., Llaca V., Karn A., Gouker F., Cadle-Davidson L., Reisch B., Fennell A., Cantu D., Sun Q., Londo J.P. (2021). Multiple independent recombinations led to hermaphroditism in grapevine. Proceedings of the National Academy of Sciences 118(15).
Naegele R.P., Londo J.P., Zou C., Cousins P. (2021). Identification of SNPs associated with magnesium and sodium uptake and the effect of their accumulation on micro and macro nutrient levels in Vitis vinifera. PeerJ 9, e10773.
Chitwood D.H., Mullins J., Migicovsky Z., Frank M., VanBuren R., Londo J.P. (2021). Vein‐to‐blade ratio is an allometric indicator of leaf size and plasticity. American Journal of Botany 108(4), 571-579.
Bryson A.E., Wilson Brown M., Mullins J., Dong W., Bahmani K., Bornowski N., Chiu C., Engelgau P., Gettings B., Gomezcano F., Gregory L.M., Haber A.C., Hoh D., Jennings E.E., Ji Z., Kaur P., Kenchanmane Raju S.K., Long Y., Lotreck S.G., Mathieu D.T., Ranaweera T., Ritter E.J., Sadohara R., Shrote R.Z., Smith K.E., Teresi S.J., Venegas J., Wang H., Wilson M.L., Tarrant A.R., Frank M.H., Migicovsky Z., Kumar J., VanBuren R., Londo J.P., Chitwood D.H. (2020). Composite modeling of leaf shape along shoots discriminates Vitis species better than individual leaves. Applications in Plant Sciences 8(12).
Bhattarai G., Fennell A., Londo J.P., Coleman C., Kovacs L.G. (2020). A Novel Grape Downy Mildew Resistance Locus fromVitis rupestris. American Journal of Enology and Viticulture 72(1), 12-20.
Patel S., Robben M., Fennell A., Londo J.P., Alahakoon D., Villegas-Diaz R., Swaminathan P. (2020). Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’. Horticulture Research 7(1).
Zou C., Karn A., Reisch B., Nguyen A., Sun Y., Bao Y., Campbell M.S., Church D., Williams S., Xu X., Ledbetter C.A., Patel S., Fennell A., Glaubitz J.C., Clark M., Ware D., Londo J.P., Sun Q., Cadle-Davidson L. (2020). Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nature Communications 11(1).
Yang Y., Cuenca J., Wang N., Liang Z., Sun H., Gutierrez B., Xi X., Arro J., Wang Y., Fan P., Londo J., Cousins P., Li S., Fei Z., Zhong G.Y. (2020). A key ‘foxy’ aroma gene is regulated by homology-induced promoter indels in the iconic juice grape ‘Concord’. Horticulture Research 7(1).
Demmings E.M., Williams B.R., Lee C.R., Barba P., Yang S., Hwang C.F., Reisch B.I., Chitwood D.H., Londo J.P. (2019). Quantitative Trait Locus Analysis of Leaf Morphology Indicates Conserved Shape Loci in Grapevine. Frontiers in Plant Science 10.
Kovaleski A.P., Londo J.P. (2019). Tempo of gene regulation in wild and cultivated Vitis species shows coordination between cold deacclimation and budbreak. Plant Science 287, 110178.
Kovaleski A.P., Londo J.P., Finkelstein K.D. (2019). X-ray phase contrast imaging of Vitis spp. buds shows freezing pattern and correlation between volume and cold hardiness. Scientific Reports 9(1).
Li M., Klein L.L., Duncan K.E., Jiang N., Chitwood D.H., Londo J.P., Miller A.J., Topp C.N. (2019). Characterizing 3D inflorescence architecture in grapevine using X-ray imaging and advanced morphometrics: implications for understanding cluster density. Journal of Experimental Botany 70(21), 6261-6276.
Londo J.P., Kovaleski A.P. (2019). Deconstructing cold hardiness: variation in supercooling ability and chilling requirements in the wild grapevine Vitis riparia. Australian Journal of Grape and Wine Research 25(3), 276-285.
Migicovsky Z., Harris Z.N., Klein L.L., Li M., McDermaid A., Chitwood D.H., Fennell A., Kovacs L.G., Kwasniewski M., Londo J.P., Ma Q., Miller A.J. (2019). Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard. Horticulture Research 6(1).
Kovaleski A.P., Reisch B.I., Londo J.P. (2018). Deacclimation kinetics as a quantitative phenotype for delineating the dormancy transition and thermal efficiency for budbreak in Vitis species. AoB PLANTS.
Li M., An H., Angelovici R., Bagaza C., Batushansky A., Clark L., Coneva V., Donoghue M.J., Edwards E., Fajardo D., Fang H., Frank M.H., Gallaher T., Gebken S., Hill T., Jansky S., Kaur B., Klahs P.C., Klein L.L., Kuraparthy V., Londo J., Migicovsky Z., Miller A., Mohn R., Myles S., Otoni W.C., Pires J.C., Rieffer E., Schmerler S., Spriggs E., Topp C.N., Van Deynze A., Zhang K., Zhu L., Zink B.M., Chitwood D.H. (2018). Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace. Frontiers in Plant Science 9.
Londo J.P., Kovaleski A.P., Lillis J.A. (2018). Divergence in the transcriptional landscape between low temperature and freeze shock in cultivated grapevine (Vitis vinifera). Horticulture Research 5(1).
Klein L.L., Miller A.J., Ciotir C., Hyma K., Uribe‐Convers S., Londo J. (2018). High‐throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections. American Journal of Botany 105(2), 215-226.
Shellie K., Kovaleski A.P., Londo J.P. (2018). Water deficit severity during berry development alters timing of dormancy transitions in wine grape cultivar Malbec. Scientia Horticulturae 232, 226-230.
Thompson T., Petersen S., Londo J., Qiu W.P. (2018). First Report of Grapevine red blotch virus in Seven Vitis Species in a U.S. Vitis Germplasm Repository. Plant Disease 102(4), 828-828.
Fresnedo-Ramírez J., Yang S., Sun Q., Cote L.M., Schweitzer P.A., Reisch B.I., Ledbetter C.A., Luby J.J., Clark M.D., Londo J.P., Gadoury D.M., Kozma P., Cadle-Davidson L. (2017). An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci. Molecular Breeding 37(12).
Harris Z.N., Kovacs L.G., Londo J.P. (2017). RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’. BMC Genomics 18(1).
Londo J.P., Kovaleski A.P. (2017). Characterization of Wild North American Grapevine Cold Hardiness Using Differential Thermal Analysis. American Journal of Enology and Viticulture 68(2), 203-212.
Adam-Blondon A.F., Alaux M., Pommier C., Cantu D., Cheng Z.M., Cramer G., Davies C., Delrot S., Deluc L., Di Gaspero G., Grimplet J., Fennell A., Londo J., Kersey P., Mattivi F., Naithani S., Neveu P., Nikolski M., Pezzotti M., Reisch B., Töpfer R., Vivier M., Ware D., Quesneville H. (2016). Towards an open grapevine information system. Horticulture Research 3(1).
Centinari M., Smith M.S., Londo J.P. (2016). Assessment of Freeze Injury of Grapevine Green Tissues in Response to Cultivars and a Cryoprotectant Product. HortScience 51(7), 856-860.
Fresnedo-Ramírez J., Sun Q., Hwang C.F., Ledbetter C.A., Ramming D.W., Fennell A.Y., Walker M.A., Luby J.J., Clark M.D., Londo J.P., Cadle-Davidson L., Zhong G.Y., Reisch B.I. (2016). Toward the elucidation of cytoplasmic diversity in North American grape breeding programs. Molecular Breeding 36(8).
Yang S., Fresnedo-Ramírez J., Wang M., Cote L., Schweitzer P., Barba P., Takacs E.M., Clark M., Luby J., Manns D.C., Sacks G., Mansfield A.K., Londo J., Fennell A., Gadoury D., Reisch B., Cadle-Davidson L., Sun Q. (2016). A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine. Horticulture Research 3(1).
Chitwood D.H., Rundell S.M., Li D.Y., Woodford Q.L., Yu T.T., Lopez J.R., Greenblatt D., Kang J., Londo J.P. (2016). Climate and Developmental Plasticity: Interannual Variability in Grapevine Leaf Morphology. Plant Physiology 170(3), 1480-1491.
Yang S., Fresnedo-Ramírez J., Sun Q., Manns D.C., Sacks G.L., Mansfield A.K., Luby J.J., Londo J.P., Reisch B.I., Cadle-Davidson L.E., Fennell A.Y. (2016). Next Generation Mapping of Enological Traits in an F2 Interspecific Grapevine Hybrid Family. PLOS ONE 11(3), e0149560.
Warschefsky E.J., Klein L.L., Frank M.H., Chitwood D.H., Londo J.P., von Wettberg E.J.B., Miller A.J. (2016). Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes. Trends in Plant Science 21(5), 418-437.
Chitwood D.H., Klein L.L., O'Hanlon R., Chacko S., Greg M., Kitchen C., Miller A.J., Londo J.P. (2015). Latent developmental and evolutionary shapes embedded within the grapevine leaf. New Phytologist 210(1), 343-355.
Hyma K.E., Barba P., Wang M., Londo J.P., Acharya C.B., Mitchell S.E., Sun Q., Reisch B., Cadle-Davidson L. (2015). Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine. PLOS ONE 10(8), e0134880.
Moyer M.M., Londo J., Gadoury D.M., Cadle-Davidson L. (2015). Cold Stress-Induced Disease Resistance (SIDR): indirect effects of low temperatures on host-pathogen interactions and disease progress in the grapevine powdery mildew pathosystem. European Journal of Plant Pathology 144(4), 695-705.
Pap D., Miller A.J., Londo J.P., Kovács L.G. (2015). Population Structure of Vitis rupestris, an Important Resource for Viticulture. American Journal of Enology and Viticulture 66(4), 403-410.
Sagers C., Londo J., Bautista N., Lee E., Watrud L., King G. (2015). Benefits of Transgenic Insect Resistance in Brassica Hybrids under Selection. Agronomy 5(1), 21-34.
Londo J.P., Garris A.M. (2014). Genetic and protein sequence variation of CBF1-4 in cold hardy wild grapevine germplasm. VITIS 53(4), 201-206.
Wang L., Zhu W., Fang L., Sun X., Su L., Liang Z., Wang N., Londo J.P., Li S., Xin H. (2014). Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera. BMC Plant Biology 14(1).
Londo J., McKinney J., Schwartz M., Bollman M., Sagers C., Watrud L. (2014). Sub-lethal glyphosate exposure alters flowering phenology and causes transient male-sterility in Brassica spp. BMC Plant Biology 14(1), 70.
Londo J.P., Johnson L.M. (2014). Variation in the chilling requirement and budburst rate of wild Vitis species. Environmental and Experimental Botany 106, 138-147.
Xin H., Zhu W., Wang L., Xiang Y., Fang L., Li J., Sun X., Wang N., Londo J.P., Li S. (2013). Genome Wide Transcriptional Profile Analysis of Vitis amurensis and Vitis vinifera in Response to Cold Stress. PLoS ONE 8(3), e58740.
Londo J.P., Bollman M.A., Sagers C.L., Lee E.H., Watrud L.S. (2011). Changes in fitness-associated traits due to the stacking of transgenic glyphosate resistance and insect resistance in Brassica napus L. Heredity 107(4), 328-337.
Londo J.P., Bollman M.A., Sagers C.L., Lee E.H., Watrud L.S. (2011). Glyphosate‐drift but not herbivory alters the rate of transgene flow from single and stacked trait transgenic canola (Brassica napus) to nontransgenic B. napus and B. rapa. New Phytologist 191(3), 840-849.
Schafer M.G., Ross A.A., Londo J.P., Burdick C.A., Lee E.H., Travers S.E., Van de Water P.K., Sagers C.L. (2011). The Establishment of Genetically Engineered Canola Populations in the U.S. PLoS ONE 6(10), e25736.
Reichman J.R., Smith B.M., Londo J.P., Bollman M.A., Auer C.A., Watrud L.S. (2011). Diallelic Nuclear Microsatellites for Diversity and Population Analyses of the Allotetraploid Creeping Bentgrass (Agrostis stolonifera). Crop Science 51(2), 747-758.
Watrud L.S., King G., Londo J.P., Colasanti R., Smith B.M., Waschmann R.S., Lee E.H. (2011). Changes in constructedBrassicacommunities treated with glyphosate drift. Ecological Applications 21(2), 525-538.
Londo J.P., Bautista N.S., Sagers C.L., Lee E.H., Watrud L.S. (2010). Glyphosate drift promotes changes in fitness and transgene gene flow in canola (Brassica napus) and hybrids. Annals of Botany 106(6), 957-965.
LONDO J.P., SCHAAL B.A. (2007). Origins and population genetics of weedy red rice in the USA. Molecular Ecology 16(21), 4523-4535.
Londo J.P., Chiang Y.C., Hung K.H., Chiang T.Y., Schaal B.A. (2006). Phylogeography of Asian wild rice, Oryza rufipogon , reveals multiple independent domestications of cultivated rice, Oryza sativa. Proceedings of the National Academy of Sciences 103(25), 9578-9583.
Gaskin J.F., Ryan F.J., Hrusa G.F., Londo J.P. (2006). Genotype diversity of Salsola tragus and potential origins of a previously unidentified invasive Salsola from California and Arizona. Madroño 53(3), 246-253.
Gaskin J.F., Ghadremani-nejad F., Zhang D., Londo J.P. (2004). A systematic overview of Frankeniaceae and Tamaricaceae from nuclear rDNA and plastid sequence data. Annals of the Missouri Botanical Garden 91(3), 401-409.