Exon based amplified polymorphism (EBAP): A novel and universal molecular marker for plants

Abstract

Background: Exons are an important part of genes. However, there has been no molecular marker technique based on single primer amplification developed for exons region.

Results: A novel molecular marker technique called exon based amplified polymorphism (EBAP) which used single primer to perform the PCR was developed. Single primers were designed based on the rich GC bases in the exon region of genes. The single primer consists of filling sequence, intermediate core region sequence and selective bases sequence. The filling sequence has a total of six bases, which can be 2A and 2T or 3A and 3T. The intermediate core region sequence consists of eight bases, all of which are G and C, but at least 2G or 2C are required. The first of the three selective bases must be either A or T, and the second and third are arbitrary bases. Due to the principle of primer design, these single primers should be universal. We applied it to the DNA polymorphisms detection of maize, sugarcane, potato, cassava, cabbage, and peanut. The results showed that it detected more abundant DNA polymorphisms in the first five crops, but not in the cultivated peanut. In addition, different band patterns were obtained by amplifying peanut cDNA with different single primers.

Conclusions: We have developed a novel and universal molecular marker technique. It is simple, fast and efficient. It does not require genomic sequence information. It can be widely used in germplasm identification, genetic diversity analysis, and molecular fingerprinting.