ORIGINAL PAPER Quantitative proteomic analysis of short photoperiod and low-temperature responses in bark tissues of peach (Prunus persica L. Batsch) Jenny Renaut & Jean-François Hausman & Carole Bassett & Timothy Artlip & Henry-Michel Cauchie & Erwin Witters & Michael Wisniewski Received: 23 April 2007 / Revised: 15 December 2007 / Accepted: 16 December 2007 / Published online: 13 February 2008 # Springer-Verlag 2008 Abstract In the temperate climate of the northern hemi- sphere, winter survival of woody plants is determined by the ability to acclimate to freezing temperatures and to undergo a period of dormancy. Cold acclimation in many woody plants is initially induced by short photoperiod and low, non-freezing temperatures. These two factors (5°C and short photoperiod) were used to study changes in the proteome of bark tissues of 1-year-old peach trees. Difference in-gel electrophoresis technology, a gel-based approach involving the labeling of proteins with different fluorescent dyes, was used to conduct a quantitative assessment of changes in the peach bark proteome during cold acclimation. Using this approach, we were able to identify differentially expressed proteins and to assign them to a class of either ‘temperature-responsive’ or ‘photoperiod- responsive’ proteins. The most significant factor affecting the proteome appeared to be low temperature, while the combi- nation of low temperature and short photoperiod was shown to act either synergistically or additively on the expression of some proteins. Fifty-seven protein spots on gels were identified by mass spectrometry. They included proteins involved in carbohydrate metabolism (e.g., enolase, malate dehydrogenase, etc), defense or protective mechanisms (e.g., dehydrin, HSPs, and PR-proteins), energy production and electron transport (e.g., adenosine triphosphate synthases and lyases), and cytoskeleton organization (e.g., tubulins and actins). The information derived from the analysis of the proteome is discussed as a function of the two treatment factors: low temperature and short photoperiod. Keywords Proteome . Cold hardiness . Cold acclimation Abbreviations 2D (E) bidimensional (electrophoresis) ABA abscisic acid CHAPS 3-([3-cholamidopropyl]dimethylammonio)- 1-propanesulfonate DiGE difference in-gel electrophoresis DTT dithiothreitol HSP heat-shock protein IPG immobilized pH gradient LD long day LT low temperature Tree Genetics & Genomes (2008) 4:589–600 DOI 10.1007/s11295-008-0134-4 Electronic supplementary material The online version of this article (doi:10.1007/s11295–008–0134-4) contains supplementary material, which is available to authorized users. Communicated by R. Sederoff J. Renaut (*) : J.-F. Hausman : H.-M. Cauchie Department of Environment and Agrobiotechnologies, Centre de Recherche Public–Gabriel Lippmann, 41 rue du Brill, 4422, Belvaux, GD Luxembourg e-mail: renaut@lippmann.lu C. Bassett : T. Artlip : M. Wisniewski Appalachian Fruit Research Station, Agricultural Research Service, US Department of Agriculture, 2217 Wiltshire Road, Kearneysville, WV 25430, USA E. Witters Center for Proteome Analysis and Mass Spectrometry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium