Inter- and intraspecific sequence variations of the chloroplast genome in wild and cultivated Raphanus

To assess the differentiation of the chloroplast genome in wild and cultivated species of Raphanus , nucleotide sequence polymorphisms were investigated for approximately 2 kbp ranging from trnL (UAA) to psbG in R. raphanistrum and R. sativus . Eighteen plants of wild species, 10 Japanese wild radish plants ( R. sativus ), and 31 cultivated plants were used for sequence analysis. Intraspecific variations of the chloroplast genome were present both in wild and cultivated Raphanus . All three genes investigated ( trnL , trnF and ndhJ ) contained nucleotide substitutions within the genus. Whereas, larger numbers of mutations were observed in the intergenic regions. Using the detected variations, the 59 radish plants were classified into 11 haplotypes, seven of which were unique to wild species. Among the haplotypes, one type corresponded completely with the Ogura male sterile cytoplasm. All the cultivated radishes belonged to one of four types, of which three were also observed in Japanese wild radish. The haplotypes were classified into four groups by cluster analysis, and the distribution in the dendrogram confirmed that cultivated radish has multiple origins. On the other hand, the seven haplotypes uniquely observed in R. raphanistrum were considered as useful materials to provide genetic diversity of cytoplasm for breeding of cultivated radishes.