PXD063668

PXD063668 is an original dataset announced via ProteomeXchange.

Title	Cross-Species Rhizome Proteomics Uncovers Conserved Freezing-Tolerance Strategies in Temperate Prairie Grasses: Insights for Improving Maize Cold Tolerance
Description	Early maize planting requires cold tolerance in temperate regions, which is not present in current elite maize. By extending the growing season of annual crops, net primary productivity and yield can be improved and the mismatch between soil nitrate availability and crop nitrate demand can be addressed. Wild PACMAD grasses have each independently evolved freezing tolerance. To uncover the molecular basis of this convergence, we performed TMT‐based shotgun proteomics on rhizome tissues—a perennial storage organ—sampled during winter dormancy and summer activity from five species: Panicum virgatum, Andropogon gerardii, Miscanthus giganteus, Sorghastrum nutans and Tripsacum (maize’s sister genus), all grown in Ithaca, NY (where winter lows reach –29 °C). From between ~2,400 and 4,500 proteins quantified per species per season, 330 protein families showed consistent upregulation in winter, yet only three—late embryogenesis abundant 3 (LEA3), aldose reductase, and phosphatidylethanolamine‐binding protein (PEBP)—were shared across all five lineages. Functional enrichment highlighted recurrent use of lipid transfer proteins, heat shock proteins, LEAs, and other drought‐associated cryoprotectants. Comparing rhizome proteomic data with tissue‐specific mRNA expression surprisingly revealed Tripsacum seedling leaf tissues showed substantially higher transcriptional responsiveness to cold than underground tissues, a pattern less pronounced in cold sensitive maize seedlings. Overall, the independent evolution of rhizome frost tolerance in PACMAD grasses appears to be governed by similar mechanisms driven primarily by expression‐level changes and complemented by protein structural adaptations—particularly within the LEA family—offering candidate targets for improving freezing tolerance in maize.
HostingRepository	PRIDE
AnnounceDate	2026-01-23
AnnouncementXML	Submission_2026-01-23_15:00:38.866.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Qin Fu
SpeciesList	scientific name: Tripsacum dactyloides; NCBI TaxID: NCBITaxon:4563; scientific name: Panicum virgatum; NCBI TaxID: NCBITaxon:38727; scientific name: Miscanthus x giganteus; NCBI TaxID: NCBITaxon:183674; scientific name: Andropogon gerardi; NCBI TaxID: NCBITaxon:79824; scientific name: Sorghastrum nutans; NCBI TaxID: NCBITaxon:79857;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-06 09:51:13	ID requested
⏵ 1	2026-01-23 15:00:39	announced

Dataset with its publication pending

submitter keyword: None

Qin Fu
contact affiliation	Cornell University
contact email	qf44@cornell.edu
lab head
Qin Fu
contact affiliation	Cornell University
contact email	qf44@cornell.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/01/PXD063668

PRIDE project URI

• PRIDE
  1. PXD063668
     1. Label: PRIDE project
     2. Name: Cross-Species Rhizome Proteomics Uncovers Conserved Freezing-Tolerance Strategies in Temperate Prairie Grasses: Insights for Improving Maize Cold Tolerance