CAPS markers in plant biology

Abstract

Cleaved Amplified Polymorphic Sequences (CAPS) markers are applicable in a wide range of tasks in plant biology. They were developed recently for plant genetics and breeding and have become especially useful. This mini-review contains an analysis of the information on the application of CAPS markers from the past 3–5 years. In the study presented, special attention was focused on CAPS markers linked with genes controlling important agricultural traits in different crops. The main principles of the development and analysis of CAPS markers as well as advantages and disadvantages of this type of molecular markers are briefly addressed in the beginning of this review. CAPS markers are based on PCR-amplifications of DNA fragments with specific primers, after the digestion of restriction enzymes and separation of the products in an agarose gel. Functional CAPS markers can be developed on the known sequence of a Gene of Interest for the analysis of its structure, function, expression and regulation. CAPS closely linked to the Gene of Interest are especially helpful for Marker-Assisted Selection, and they are widely used in the breeding of wheat, barley, soybean, potato, tomato and other crops for the tolerance to various pathogens. CAPS markers are often used for the preparation of genetic maps and fine mapping of studied genes. Molecular-genetic maps were prepared for some plants using CAPS. This method was also successfully used for the mapping of both individual genes and QTLs controlling such important traits as plant development, grain quality and tolerance to pathogens in cereals, as well as shape of tomato fruit. CAPS have important applications in the analyses of genetic polymorphism and phylogeny, especially in closely related species. Thus CAPS can be used as an effective tool for molecular-genetic study and plant breeding.