Biology Reference
In-Depth Information
Chapter 49
Proteotyping of Holm Oak (
Quercus ilex
subsp.
ballota
)
Provenances Through Proteomic Analysis of Acorn Flour
José Valero Galván , Raquel González Fernández , Luis Valledor ,
Rafael Ma. Navarro Cerrillo , and Jesus V. Jorrin-Novo
Abstract
Proteomics has become a powerful tool to characterize biodiversity and natural variability in plant species,
as well as to catalogue and establish phylogenetic relationships and distances among populations, prove-
nances or ecotypes. In this chapter, we describe the standard proteomics workfl ow that we currently use in
cataloguing Holm oak (
Quercus ilex
subsp.
ballota
[Desf.] Samp.) populations. Proteins are extracted from
acorn fl our or pollen by TCA/acetone or TCA/acetone-phenol methods, resolved by one- or two-
dimensional gel electrophoresis, and gel images are captured and analyzed by appropriate software and
statistical packages. Quantitative or qualitative variable bands or spots are subjected to MS analysis in order
to identify them and correlate differences in the protein profi le with the phenotypes or environmental
conditions.
Key words
Holm oak proteomics, Plant biodiversity, Plant proteotyping
1
Introduction
Electrophoresis has proven to be the most important and effective
tool in analyzing cellular protein profi les both from a quantitative
and qualitative point of view. Moreover, it is one of the most con-
venient methods for characterizing, cataloguing, and establishing
phylogenetic relationships and distances among populations, prov-
enances, ecotypes, or genotypes [
1
-
8
]. The workfl ow of a standard
1- or 2-DE-based proteomics experiment includes the following
steps: experimental design, sampling, protein extraction, protein
separation, protein analysis by mass spectrometry (MS), statistical
analysis of the data, and protein identifi cation, using proper bioin-
formatics software and tools [
9
-
11
] (Fig.
1
). The experimental
design is the key step to extracting the maximum information from
an experiment. A good experimental design considers the impact
of different sources of variation and the minimum number of rep-
licates to be made in the context of a particular minimum detectable
