MOLECULAR MARKERS ASSOCIATED WITH SPECIFIC QUANTITATIVE TRAIT LOCI (QTL) IN PLANT RESEARCH

The use of molecular markers, that allow to know the set of genes associated with a particular quantitative trait or QTL is widely extended, including: restriction fragment length polymorphism (RFLP), random-amplified polymorphic DNA (RAPD), cleaved amplified polymorphic sequences (CAPS), amplified fragment length polymorphism (AFLP), microsatellites, and single-nucleotide polymorphisms (SNPs). In addition to classical methodology, new approaches based on the next generation sequencing (NGS) methodology that enables rapid sequencing of the base pairs in DNA or RNA samples, are proving to be fundamental. SNPs have become the focus of a large number of studies designed to identify critical differences in DNA sequence that contribute to phenotypic variation for specific traits. Methods for the analysis of SNPs comprise two distinct steps, one for allele discrimination and one for allele detection. This review article describes the methods available for allele discrimination based on hybridization, primer extension, ligation and enzymatic cleavage, as well as, RAPD and CAPS molecular markers analysis.