Reverse random amplified microsatellite polymorphism reveals enhanced polymorphisms in the 3' end of simple sequence repeats in the pepper genome

• Published in: Molecules and cells Vol. 26; no. 3; pp. 250 - 257
• Main Authors: Min, W.K. (Seoul National University, Seoul, Republic of Korea), Han, J.H. (Seoul National University, Seoul, Republic of Korea), Kang, W.H. (Seoul National University, Seoul, Republic of Korea), Lee, H.R. (Seoul National University, Seoul, Republic of Korea), Kim, B.D. (Seoul National University, Seoul, Republic of Korea), E-mail: kimbd@snu.ac.kr
• Format: Journal Article
• Language: English
• Published: United States 한국분자세포생물학회 30.09.2008
• Subjects: 3' Flanking Region - genetics; Base Sequence; Capsicum - genetics; CARTE GENETIQUE; Chromosome Mapping; DNA, Plant - genetics; Genetic Linkage; GENETIC MAPS; MAPAS GENETICOS; MICROSATELITES; MICROSATELLITE; Microsatellite Repeats - genetics; MICROSATELLITES; Molecular Sequence Data; PEPPER; PIMIENTA; POIVRE; Polymorphism, Genetic; Random Amplified Polymorphic DNA Technique; reverse random amplified microsatellite polymorphism; SSR; 생물학
• ISSN: 1016-8478; 0219-1032; 0219-1032
• DOI: 10.1016/S1016-8478(23)13992-6

Microsatellites or simple sequence repeats (SSR) are widely distributed in eukaryotic genomes and are informative genetic markers. Despite many advantages of SSR markers such as a high degree of allelic polymorphisms, co-dominant inheritance, multi-allelism, and genome-wide coverage in various plant species, they also have shortcomings such as low polymorphic rates between genetically close lines, especially in Capsicum annuum. We developed an alternative technique to SSR by normalizing and alternating anchored primers in random amplified microsatellite polymorphisms (RAMP). This technique, designated reverse random amplified microsatellite polymorphism (rRAMP), allows the detection of nucleotide variation in the 3' region flanking an SSR using normalized anchored and random primer combinations. The reproducibility and frequency of polymorphic loci in rRAMP was vigorously enhanced by translocation of the 5' anchor of repeat sequences to the 3' end position and selective use of moderate arbitrary primers. In our study, the PCR banding pattern of rRAMP was highly dependent on the frequency of repeat motifs and primer combinations with random primers. Linkage analysis showed that rRAMP markers were well scattered on an intra-specific pepper map. Based on these results, we suggest that this technique is useful for studying genetic diversity, molecular fingerprinting, and rapidly constructing molecular maps for diverse plant species.