**1. Introduction**

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Relationships

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Soybean (*Glycine max* L. Merrill) is one of the most important and most cultivated crops in the world, with significant quantities of proteins being found in their yield composition, around 40% of their yield dry matter. This expressive quantity of proteins, and also a con‐ siderable percentage of oil, around 21% of their dry matter, has turned this grain into a product of great importance for the industrial sector, whether it be for food, cosmetics or, more recently, biofuels. Thus, soybean breeding programs directed toward these areas be‐ come ever more important, together with agronomic characteristics that allow greater pro‐ ductivity in sustainability with the environment in which they are produced.

The achievement of soybean genome sequencing [1], facilitated by identification of the ge‐ netic base, lead to advances in obtaining improved cultivars through knowledge of the com‐ plete sequence of expressed genes. Nevertheless, this information is not sufficient to identify which proteins are really being expressed in the cell at a given moment and under a certain condition since, through the phenomenon of splicing, different proteins may be produced by alteration of the command of a single gene. Thus, the complementary DNA (cDNA) and the messenger RNA (mRNA) have come to be the main focus of study for obtaining infor‐ mation regarding genetic expression or transcriptome. Nevertheless, due to post-translation‐ al regulation mechanisms, the quantity of expressed protein is not necessarily proportional to the quantity of its corresponding mRNA, which often raises questions regarding the role of this gene in cellular metabolism.

The reason for this is that control of gene expression occurs from mRNA transcription up to post-translational modifications like glycosylation and phosphorylation, among other proc‐ esses, which alter protein activity (Figure 1).

© 2013 Fortes Gris and Baldoni; licensee InTech. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2013 Fortes Gris and Baldoni; licensee InTech. This is a paper distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

In recent years, for the purpose of complementing the information obtained by means of ge‐ nome sequencing and transcriptome, proteomics, one of the dimensions of the post-genome era [2], arises with a set of highly powerful techniques for separation and identification of proteins in biological samples, allowing better understanding of the networks of cellular op‐ eration and regulation upon representing the link between the genotype and the phenotype of an organism.

For the aforementioned reasons, proteomic analysis is now one of the most efficient means for functional study of the genes and genomes of complex organisms [3]. This has generated new data, as well as validated, complemented and even corrected information obtained through other approaches, thus contributing to better understanding of plant biology.

**Figure 1.** Pathways in which gene and protein expression may be regulated or modified in transcription or in posttranslation [13].

Its study involves the entire set of proteins expressed by the genome of a cell, or only those that are expressed differentially under specific conditions. Also it is directed to the set of protein isoforms and post-translational modifications, to the interactions among them, as well as to the structural description of molecules and their complexes.

Bidimensional electrophoresis and mass spectrometry are the core technologies of proteo‐ mics, although new methodologies are being applied to plants for specific studies [4,5,6]. Among the most recent proteomic techniques are Difference Gel Electrophoresis (DIGE) and Multi-dimensional Protein Identification Tecnology (MudPIT), used in separation of pro‐ teins from a complex mixture. Other methods involved are Stable Isotopic Labeling using Amino Acids in Cell Culture (SILAC), Isotope Coded Affinity Tag (ICAT) and Isobaric Tag for Relative and Absolute Quantitation (iTRAQ) are based on labeling with isotopes for quantification of molecules by mass spectrometry.

In spite of the recent nature of research in this area, diverse studies with soybeans using pro‐ teomic tools are being performed throughout the world, showing this to be a promising area for selection of genotypes for genetic breeding programs [7,8]. Moreover, the study of plant responses to infections from pathogens has supplied significant data for understanding the signaling process that triggers the defense response in plants [9]. Additionally, there are studies characterizing the proteome of plants in response to different stress conditions aris‐ ing from both abiotic factors [10] and biotic factors [11]. These comparative studies of con‐ trasting genotypes for a determined type of stress allow identification of the proteins that respond to stress by means of changes in their levels of expression. Identifying these mole‐ cules and their respective functions, the work of breeding is directed and should have con‐ tinuity only with those molecules that perform roles related to the characteristic of stress tolerance. For that reason, it is essential to cross the proteomic data with information also obtained by genomics, transcriptomics and metabolomics, so as to verify the correlation of the candidate proteins with the desired characteristic.

In relation to products derived from genetically modified foods, proteomic techniques have been applied to allow a broad approach and the analysis of many variables simultaneously in a single sample. There are also other studies relating the proteome expressed during de‐ velopment of the plants, as well as research in which soybeans have been the target of inves‐ tigations regarding nutritional, toxicological and allergenic aspects, above all on genetically modified varieties [12].This makes for increased use of this technique in biosecurity studies. In this context, the objective of this chapter is to present the main technologies used in pro‐ teomic studies in diverse areas of activity, as well as the main scientific results obtained in the search for superior soybean genotypes.
