Analysis of PolA1 intron 19 and Ntag sequences reveals two ancestral lineages in the origin of the Brassica rapa complex and Chinese cabbage (B. rapa var. pekinensis)

Abstract

SummaryBrassica rapa L. used to be classified into two species, Brassica campestris and B. rapa.These two species can cross with each other, but no molecular marker exists to discriminate between them. Therefore, these two species are now combined into one species, B. rapa. Because nuclear genomes have been genetically recombined through repeated inter-specific hybridisation, most DNA sequences have lost the characteristics unique to each species. Thus, in order to trace an evolutionary lineage, it is important to analyse a DNA sequence that rarely recombines during meiosis in inter-specific hybrids. Sequences of the nineteenth intron of the PolA1 gene in 33 accessions of B. rapa, encoding the largest subunit of RNA polymerase I, showed either short (S; 183 bp) or long (L; 242 bp) type sequences. Nucleotide tag (Ntag) sequences, the protein-coding sequence (ca. 1.2 kb) from exons 19 - 21 of the PolA1 gene, in 20 accessions, were also classified into the same S- or L-types. Detailed sequence analysis showed that 13 single nucleotide polymorphisms (SNPs) in the 5'-half of the Ntag sequence did not recombine between the S- and L-types.These data suggest that two ancestral lineages were present and were probably involved in the origin of Chinese cabbage because accessions of B. rapa var. pekinensis had PolA1 gene sequences of either the S- or L-type, or both. Two accessions of B. napus var. rapifera (2n = 38) showed both the S- and L-types of B. rapa (2n = 20), indicating that this species might be an allotetraploid between the two ancestral lineages, followed by two chromosome deletions.