**5. New markers**

The possibility of manipulation of genetic material, derived from discoveries as plasmids, restriction enzymes and the enzyme reverse trasncriptase led to the development of RFLP markers. The PCR technique revolutionized the field of studies on molecular markers and allowed the studies that led to the development of RAPD, microsatellites and AFLP, described in the chapter.

The speed of evolution of knowledge, provided by the large number of studies, development of equipment, reagent delivery and qualification of researchers put it, every day, new tools available to the scientific community. No doubt the generation of knowledge is beneficial and desirable, but the constant changes lead to the need for updates, especially laboratories, which is not always possible. In this line of reasoning, are presented some of the newer molecular markers.

The development of markers in the studies reveals the possibility of treating areas with occasional changes, such as a molecular marker. A Single Nucleotide Polymorphism or SNP is a small change or variation that may occur in a DNA sequence in a significant portion (more than 1%) of a population.

SNPs are the most frequent forms of genetic variations. Approximately 90% of human genetic variations are SNPs that occur every 300 ~ 600 nucleotides and has become markers of choice for its high abundance and development of technologies for large-scale genotyping as microarray hybridization, primer extension, and connection. SNPs are changes in DNA that are maintained in future generations, the mutation was distinguished by being present with a range greater than 1%. When the mutation is set at a minimum frequency of 1% is considered a SNP (Kwok & Gu, 1999).

reducing the time required to obtain an acceptable recovery of the recurrent parent (Borém & Miranda, 2005). The proportion of recurrent parent obtained in the first backcross generation, after selection of a marker in each of the chromosomes of tomato, roughly equals the proportion in three backcross generations in the absence of selection (Tankskey & Rick,

Genetic characterization: Description of a plant gene in their DNA. Molecular methods allow the varietal characterization with high discrimination power. Several studies have shown the quality of information on the molecular identification of germplasm (Lee et

Marker-assisted selection: The possibility of identifying genes of interest, to be strongly linked to molecular markers allows the selection can be made indirectly. In cases where gene expression occurs only in the final phase of the cycle of the species, such as the lipoxygenase in soybeans, the possibility of indirect selection through molecular markers becomes attractive (Borém & Miranda, 2005). The same authors reported useful for screening individuals who have two or more genes whose expression produces similar

Great prospects for the area of molecular markers have been discussed. The potential usefulness of these techniques will be achieved, for example, through indirect selection based on markers: when the desired character has low heritability or present difficult evaluation, in situations where there are undesirable genetic correlations between traits, and especially the practice of early selection in crops perennials. The isolation, cloning and manipulation of individual genes that control quantitative traits of economic importance is a

The possibility of manipulation of genetic material, derived from discoveries as plasmids, restriction enzymes and the enzyme reverse trasncriptase led to the development of RFLP markers. The PCR technique revolutionized the field of studies on molecular markers and allowed the studies that led to the development of RAPD, microsatellites and AFLP,

The speed of evolution of knowledge, provided by the large number of studies, development of equipment, reagent delivery and qualification of researchers put it, every day, new tools available to the scientific community. No doubt the generation of knowledge is beneficial and desirable, but the constant changes lead to the need for updates, especially laboratories, which is not always possible. In this line of reasoning, are presented some of

The development of markers in the studies reveals the possibility of treating areas with occasional changes, such as a molecular marker. A Single Nucleotide Polymorphism or SNP is a small change or variation that may occur in a DNA sequence in a significant portion

SNPs are the most frequent forms of genetic variations. Approximately 90% of human genetic variations are SNPs that occur every 300 ~ 600 nucleotides and has become markers of choice for its high abundance and development of technologies for large-scale genotyping as microarray hybridization, primer extension, and connection. SNPs are changes in DNA that are maintained in future generations, the mutation was distinguished by being present with a range greater than 1%. When the mutation is set at a minimum frequency of 1% is

phenotypes, as is the case of pyramiding genes conferring resistance to a pathogen.

1980);

al.,1989; Smith & Smith, 1991).

goal, theoretically attainable.

**5. New markers** 

described in the chapter.

the newer molecular markers.

(more than 1%) of a population.

considered a SNP (Kwok & Gu, 1999).

Variations in the sequences are the result of mutations and SNPs are mutations that have spread over generations and may occur either in coding regions as in non-coding genomes. They are classified as non-synonymous when they occur in coding regions and can result in an amino acid substitution in the protein sequence. Classification as synonymous SNPs is given the changes that occur in non-coding region. These markers can be used in genotyping and as a new strategy for identification of polymorphism in species with low degree of polymorphism.

Molecular markers are very important in structural and functional genomics of animal species, plants and microorganisms. The marker developed by Hu & Vick (2003) was named Region Amplification Polymorphism Target (TRAP). It's is a fast and efficient using bioinformatics tools and data from EST's to generate polymorphic markers around targeted candidate gene sequences based on PCR. It is considered a dominant marker, which combines the ease of the RAPD markers with polymorphism of AFLP markers.

The polymorphism is generated from a combination of a fixed primer designed from an EST sequence of interest, and an arbitrary primer. Recent studies have reported the use of TRAP markers to access genetic diversity in sugarcane and identification of possible candidate genes for cold tolerance and metabolic pathway involved in sucrose (Alwala et al., 2006). The technique is extremely simply practice involving the extraction of genomic DNA and a PCR reaction.

Möller (2010) evaluated 286 F2 plants from crosses of IAC-100 and CD-215 in order to identify markers linked to genes conferring resistance to sucking bugs of soybean seeds. For the marker TRAP, 11 primer combinations fixed / arbitrary generated 230 brands, and 31 (13.48%) polymorphic, an average of 2.82 marks per polymorphic combination. Despite the lower number of different polymorphic by combining the percentage of polymorphism obtained with the marker TRAP (0.13) was higher than for AFLP (0.10).

Finally the marker Nucleotide Binding Site (NBS) which has been successfully used in potato, tomato, lettuce, barley (Van der Linden et al., 2004), allowing the identification of areas of resistance genes highly conserved between species. The technique consists of amplification of specific regions using degenerate primers homologous to conserved sequences of resistance genes (R-genes).

The visualization of fragments generated by molecular markers, is usually performed using gel electrophoresis, which can hinder the precise correlation between the bands and allelic variations. Technological developments put at the disposal of researchers, hybridization methods such as microarrays. The high cost restricts their use in most laboratories. Alternatively, we developed a methodology called: Diversity Arrays Technology (DArT), which allows analysis of genomic representations without the need for sequencing.

The technique is based on the construction of panels of diversity and hybridization microarray. Its use allows the visualization of the presence or absence of specific fragments in the genome.
