Development and evaluation of broadly applicable markers for Restorer-of-fertility in pepper

The Restorer-of-fertility (Rf) gene is used for efficient hybrid seed production in chili pepper. Although molecular markers linked to Rf in pepper are available, their applications have been limited by lack of agreement between marker genotype and phenotype. To overcome this limitation, we developed new molecular markers using an Rf-segregating population for which most of previously developed markers are not suitable, because of lack of polymorphism. The petunia Rf gene was used as a candidate for marker development. First of all, a pepper bacterial artificial chromosome (BAC) library was screened using a pepper homolog of the petunia Rf gene. The 52 selected BAC clones were classified into three contig groups and each contig group was mapped to chromosome 6. Three markers were developed using the three groups; their genetic distances from the Rf locus were 1.4, 3.2 and 14 cM, respectively. In the second place, an Rf-linked marker was developed from the sequence of a tomoto BAC clone containing three genes which are homologous to petunia Rf gene. Genetic distance between this marker and Rf gene was 1.4 cM. When newly-, and previously-developed molecular markers linked to Rf were applied to 55 pepper breeding lines, one marker named CRF-SCAR was found to be the most broadly applicable, based on correct determination of phenotypes. In the present study, we demonstrate that previously cloned Rf genes can be used as candidate genes for development of new markers for the reliable detection of restorer lines. We expect that the newly-developed markers and information obtained from application of markers will be useful for reliable detection of restorer lines.