Polymorphism of pepper (Capsicum annuum L.) seed proteins studied by two‐dimensional electrophoresis with immobilized pH gradients: Methodical and genetic aspects

A population of ten morphologically similar inbred lines of pepper (Capsicum annuum L.) has been investigated for polymorphism of seed proteins by two‐dimensional (2‐D) electrophoresis with immobilized pH gradients. To reveal as much variation as possible, both the water‐ and the urea/detergent‐soluble protein fraction were electrophoretically analyzed and subsequently visualized by silver staining. The 2‐D patterns were subjected to computer analysis to be able to establish genetic variation. A high number of the seed proteins were found to be variable as to presence/absence: these were 68 out of 184 reproducible water‐soluble proteins and 34 out of 419 reproducible urea/detergent‐soluble proteins. Comparison of the 2‐D data of the water‐soluble and the urea/detergent‐soluble proteins, which represent the biggest part of all extractable seed proteins, showed that both protein fractions have proteins in common, but the variable proteins found in both fractions were non‐identical. The difference of variability scored in both solubility fractions was discussed. Genetic distances between all pairs of inbred pepper lines were calculated and a genetic tree was constructed. A correlation analysis was carried out to correct for genetic linkage and for secondary modifications, to have a more proper estimate of genetic distances. In both cases the dendrograms showed two distinct genetic groups of five inbred lines. This electrophoretic study was done in order to utilize the genetic distance data in breeding for heterosis. The genetic distance data presented will be used to validate the assumption that there is a higher chance to achieve better hybrid performance when the genetic distance between the parents is as great as possible. From the fact that we found a high level of genetic variability within a population of ten morphologically similar inbred lines, it can be concluded that 2‐D electrophoresis can be efficiently applied in pepper breeding.