Comparison of Sequence of rbcL and Non-coding Regions of Chloroplast DNA and ITS2 Region of rDNA in Genus Humulus.

Abstract

The divergence among hop cultivars, as well as wild hops (Humulus lupulus var. lupulus, neomexicanus and cordifolius) and related species (H.japonicus) was studied using the sequence difference of the partial rbcL fragment, the noncoding regions, the trnL intron and spacer between the trnL3' exon and trnF, of chloroplast DNA and the ITS2, one of the nuclear ribosomal internal transcribed spacer regions. There were no differences within the varieties of H.lupulus and within H.japonicus. A few nucleotide substitutions were observed between the varieties of H.lupulus in the 1260 bp nucleotide sequence of rbcL or the 853 bp total of the noncoding regions of choroplast DNA. There were no nucleotide changes in the 232 bp ITS2, even though this region showed a higher substitution rate when H.lupulus and H.japonicus were compared. H.japonicus showed 13 substitutions in rbcL, 9 in the noncoding regions and 24 in the ITS2 region compared with H.lupulus var.lupulus. Synonymous substitution at tne 3rd codon position of rbcL enabled to estimate the divergence time of the two species at 3.74 million years ago. This study which revealed a low variability within H.lupulus suggests that variation, which could be utilized in hop breeding is limited.