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Abstract: Recent advances in manipulating nucleic acids have opened a new research field called plant molecular systematics. This short review provides an overview of molecular techniques which have been used in the analysis of DNA molecules for the study of plant systematics, with a special emphasis on PCR. The early application of DNA analysis, DNA/DNA hybridization, has not become popular with plant systematists, because of several disadvantages inherent in the method. The survey of restriction fragment length polymorphisms (RFLPs), on the contrary, has become one of the preferred methods used by plant molecular systematists, since the method is relatively easy to perform. Although unambiguous data can be obtained by both long-range restriction mapping and nucleotide sequencing, these approaches may have limited use in plant molecular systematics because of their laborious experimental procedures relying on conventional molecular cloning techniques. To date, PCR based analyses of the DNA molecule seem to be the most suitable experimental approach for plant molecular systematics. Several advantages of the method have changed both the quality and quantity of the DNA data. Further application of PCR to plant molecular systematics will open up a new era in the field.

To determine the origin of Ogura male sterile cytoplasm in radish (Raphanus sativus L.), wild and cultivated radishes were crossed. Three types of progeny resulted from the F1 hybrids between the wild radish from ‘Kushikino’ with Ogura-type mtDNA and the cultivars (‘Uchiki-Gensuke’ or ‘Comet’). The segregation patterns of the male sterility were compared with those of Ogura cytoplasm. The male sterility induced in the F1 hybrid was maintained by crossing with ‘Uchiki-Gensuke’, that maintains Ogura male sterility. In the two types of progeny, in which ‘Comet’ (a restorer of Ogura cytoplasm) was used as one of the parents, both fertile and sterile plants segregated at the predicted ratio on the assumption that a single dominant fertility restoring gene exists in the restorer. From these results, we concluded that the Ogura cytoplasm is identical to that of the wild radish, and the former originated in a population of Japanese wild radish.

The hot-spot region related to length mutations in the chloroplast genome of the wheat group was precisely analyzed at the DNA sequence level. This region, located downstream from the rbcL gene, was highly enriched in A+T, and contained a number of direct and inverted repeats. Many deletions/insertions were observed in the region. In most deletions/insertions of multiple nucleotides, short repeated sequences were found at the mutation points. Furthermore, a pair of short repeated sequences was also observed at the border of the translocated gene. A sequence homologous with ORF512 of tobacco cpDNA was truncated in cpDNAs of the wheat group and found only in the mitochondrial DNA of Ae. crassa, suggesting the inter-organellar translocation of this sequence. Mechanisms that could generate structural alterations of the chloroplast genome in the wheat group are discussed.

To study the maternal lineage and evolution of polyploid species of wheat, variation in mitochondrial DNA was investigated in Triticum and Aegilops by PCR-aided RFLP analysis. A 1.3 kb region containing the intron of coxII was studied using 20 accessions from five species of Sitopsis section of Aegilops, one species of Einkorn wheat, four species of tetraploid wheat, and one species of common wheat. Only three restriction site changes and a single deletion/insertion were found among 884 restriction fragments surveyed. This fact suggests the highly conserved nature of this region within Triticum and Aegilops. Four haplo-types were recognized in coxII intron. A parsimonious relationship indicated that three haplo-types were independently derived from one prototype which was found in wild Einkorn and Aegilops species except for Ae. speltoides. All but one accession of Ae. speltoides possessed a derivative haplo-type, common in Timopheevi wheat. The result supported the hypothesis that Ae. speltoides donated the G genome to Timopheevi wheat; however did not agree with that Ae. speltoides was the B genome donor to the Emmer and common wheat.