CAPS technology as a tool for the development of genic and functional markers: study in peas

DNA markers linked to economically important alleles are often used in plant breeding in order to replace/assist traditional phenotypic selection. Thanks to growing advances in agricultural genetics and genomics, it is possible today to develop so-called genic markers, designed on the DNA sequence of genes having a known effect on the phenotype, and functional markers, targeting, within the same genes, polymorphisms directly responsible for the phenotype. It is known that allelic variation is commonly due to single nucleotide polymorphisms (SNPs) and small insertion/deletions (In/Del), which in many cases can be associated to the creation or disruption of restriction endonucleases recognition sites. Thus, cleaved amplified polymorphic sequence (CAPS) technology is particularly suitable for the development of genic and functional markers. In recent activities, we developed a series of CAPS and derived CAPS (dCAPS) functional markers which target all SNP mutations in a gene of cultivated pea (Pisum sativum L.) known to determine resistance to the powdery mildew pathogen Erysiphe pisi. Molecular markers other than CAPS, including those based on next generation sequencing methods, can be today used to target SNPs and In/Del polymorphisms. However, considering their ease of obtainment without the need of costly equipment, CAPS might be still the markers of choice for breeding programs which do not make use of genome-wide screenings and for species whose genetic/genomic information is limited.