Development of molecular markers based on CRa gene sequencing of different clubroot disease-resistant cultivars of Chinese cabbage

Background CRa is a key gene in Chinese cabbage (Brassica rapa ssp. pekinensis) that confers resistance to Plasmodiophora brassicae. In order to efficiently screen the clubroot resistance (CR) gene CRa in breeding, two functional codominant markers of the CRa gene were developed. Methods and results In this study, through comparing the CRa allele sequences in resistant and susceptible cultivars of Chinese cabbage, we found two insertion and deletion of sequence variations in the fourth exon between resistant and susceptible cultivars. Two functional codominant markers for CRa gene were obtained based on the variations, namely, CRaEX04-1 and CRaEX04-3. The lengths of the extended fragment of CRaEX04-1 marker were 321 bp and 186 bp in resistant and susceptible cultivars, respectively. In contrast, those of CRaEX04-3 were 704 bp and 413 bp, respectively. We verified the genetic stability between the developed markers and CRa gene using 57 Chinese cabbage cultivars with known resistance and two genetic populations. The results showed that the marker identification was completely consistent with the known phenotypes in 57 cultivars. The marker identification results followed the 3:1 of Mendel's first law in the F-2 population, and the 1:1 of Mendel's first law in the BC1. Conclusions CRaEX04-1 and CRaEX04-3 can be used as a practical molecular marker for breeding and germplasm resource creation of clubroot disease-resistant Chinese cabbage.