Polymerase chain reaction-single strand conformational polymorphism analysis of intra- and interspecific variations in organellar DNA regions of Aegilops mutica and related species

Comparison of mitochondrial and chloroplast genome segments from three onion (Allium cepa L.) cytoplasm types and identification of a trans-splicing intron of cox2

To study genetic relatedness of two male sterility-inducing cytotypes, the phylogenetic relationship among three cytotypes of onions (Allium cepa L.) was assessed by analyzing polymorphisms of the mitochondrial DNA organization and chloroplast sequences. The atp6 gene and a small open reading frame, orf22, did not differ between the normal and CMS-T cytotypes, but two SNPs and one 4-bp insertion were identified in CMS-S cytotype. Partial sequences of the chloroplast ycf2 gene were integrated in the upstream sequence of the cob gene via short repeat sequence-mediated recombination. However, this chloroplast DNA-integrated organization was detected only in CMS-S. Interestingly, disruption of a group II intron of cox2 was identified for the first time in this study. Like other trans-splicing group II introns in mitochondrial genomes, fragmentation of the intron occurred in domain IV. Two variants of each exon1 and exon2 flanking sequences were identified. The predominant types of four variants were identical in both the normal and the CMS-T cytotypes. These predominant types existed as sublimons in CMS-S cytotypes. Altogether, no differences were identified between normal and CMS-T, but significant differences in gene organization and nucleotide sequences were identified in CMS-S, suggesting recent origin of CMS-T male-sterility from the normal cytotype.

Identification of highly variable chloroplast sequences and development of cpDNA-based molecular markers that distinguish four cytoplasm types in radish (Raphanus sativus L.)

Four types of cytoplasms (Ogura, DCGMS, DBRMF1, and DBRMF2) were identified in the previous studies using molecular markers based on mitochondrial genome variations in radish (Raphanus sativus L.). However, mtDNA markers have limitations in obtaining clear results due to complexity of radish mitochondrial genomes. To improve fidelity, molecular markers based on variation of chloroplast genome sequences were developed in this study. We searched for the sequence variations of chloroplast genome among the four cytoplasm types in 11 noncoding intergenic regions of ~8.7 kb. Highly variable intergenic regions between trnK and rps16 were identified, and a couple of 4-34 bp indels were used to develop a simple PCR-based marker that distinguished the four cytoplasm types based on the PCR product length polymorphism. Two additional cpDNA markers were developed by using a single nucleotide polymorphism and 17-bp insertion. Analysis of 90 accessions using both mtDNA and cpDNA markers showed the perfect match of results of both the markers, suggesting strict co-transmission of mitochondria and chloroplast in radish. Phylogenetic trees showed that two male-sterility inducing cytoplasms, Ogura and DCGMS, were closely related to DBRMF1 and DBRMF2, respectively. Analysis of 120 radish germplasms introduced from diverse countries showed that the frequency of male-sterility inducing mitotypes of Ogura and DCGMS was very low, and DCGMS was predominately detected in eastern European countries. Majority of accessions from Europe and Asia were shown to contain DBRMF2 and DBRMF1 mitotypes, respectively.

Heteroplasmy and paternally oriented shift of the organellar DNA composition in barley-wheat hybrids during backcrosses with wheat parents

Mitochondrial (mt) and chloroplast (ct) genome inheritance was studied in barley-wheat hybrids, as were their progenies obtained from backcrosses with different common wheat cultivars, by monitoring the composition of 4 mtDNA (coxI, a 5'-flanking region of cob, nad3-orf156, and 5'-upstream region of 18S/5S) and 2 ctDNA (simple-sequence repeat locus downstream of trnS and a 3'-flanking region of rbcL) loci. In male sterile F1 and BC1 plants, maternal barley mtDNA fragments were mainly detected and very low levels of paternal wheat fragments were occasionally detected by PCR in coxI, a 5'-flanking region of cob and nad3-orf156, whereas a 5'-upstream region of 18S/5S showed clear heteroplasmy, containing both maternal and paternal copies, with maternal copies prevailing. Plants showing such heteroplasmic mtDNA composition remained either semisterile or became completely sterile in the later backcross generations. Only maternal ctDNA copies were detected in these plants. In 3 stable, self-fertile, and vigourous lines obtained in the advanced backcross generations and possessing recombinant wheat nuclear genome, however, only mt- and ctDNA copies of wheat parents were detected; thus, the original alloplasmic condition appeared to be lost. Our results suggest that transmission followed by selective replication of the paternal wheat organellar DNA leads to a paternally oriented shift of the organellar DNA composition in barley-wheat hybrids, which correlates with the restoration of fertility and plant vigour. These 2 processes seem to be related to nucleocytoplasmic compatibility and to be under the control of the nuclear genome composition.

Characterization of genetic variation in and phylogenetic relationships among diploid Aegilops species by AFLP: incongruity of chloroplast and nuclear data

Intra- and inter-specific genetic variation was investigated in seven diploid Aegilops species using the amplified fragment length polymorphism (AFLP) technique. Of the seven species, the cross-pollinating Aegilops speltoides and Aegilops mutica showed high levels of intraspecific variation whereas the remaining five self-pollinating species showed low levels. Aegilops bicornis, Aegilops searsii and Ae. speltoides formed one cluster in the dendrograms, while Aegilops caudata and Aegilops umbellulata formed another. Relationships among the species inferred were more consistent with the relationships inferred from studies of chromosome pairing in interspecific hybrids, and previous molecular phylogenetic reconstructions based on nuclear DNA, than they were with those based on molecular plasmon analysis, suggesting that the nuclear genome has evolved differently from the cytoplasmic genome in the genus Aegilops.

ORIGIN AND TAXONOMY OF WHEAT IN THE LIGHT OF RECENT RESEARCH

There is still disagreement among scientists on the exact origin of common wheat (Triticum aestivum ssp. aestivum), one of the most important crops in the world. The first step in the development of the hexaploid aestivum group (ABD) may have been hybridisation between T. urartu (A), as pollinator, and a species related to the Sitopsis section of the Aegilops genus (S) as cytoplasm donor, leading to the creation of the tetraploid species T. turgidum ssp. dicoccoides (AB). The following step may have involved hybridisation between T. turgidum ssp. dicoccon (AB genome, cytoplasm donor), a descendant of T. turgidum ssp. dicoccoides, and Ae. tauschii (D genome, pollinator), resulting in the hexaploid species T. aestivum ssp. spelta (ABD) or some other hulled type. This form may have given rise to naked types, including T. aestivum ssp. aestivum (ABD). The ancestors of the tetraploid T. timopheevii (AG) may have been the diploid T. urartu (A genome, pollinator) and Ae. speltoides (S genome, cytoplasm donor). Species in the timopheevii group developed later than those in the turgidum group, as confirmed by the fact that the G genome is practically identical to the S genome of Ae. speltoides, while the more ancient B genome has undergone divergent evolution. Hybridisation between T. timopheevii (AG, cytoplasm donor) and T. monococcum (A m, pollinator) may have resulted in the species T. zhukovskyi (AGA m). Research into the relationships between the various species is of assistance in compiling the taxonomy of wheat and in avoiding misunderstandings arising from the fact that some species are known by two or more synonymous names.

Plasmon analyses of Triticum (wheat) and Aegilops: PCR-single-strand conformational polymorphism (PCR-SSCP) analyses of organellar DNAs

To investigate phylogenetic relationships among plasmons in Triticum and Aegilops, PCR-single-strand conformational polymorphism (PCR-SSCP) analyses were made of 14.0-kb chloroplast (ct) and 13. 7-kb mitochondrial (mt)DNA regions that were isolated from 46 alloplasmic wheat lines and one euplasmic line. These plasmons represent 31 species of the two genera. The ct and mtDNA regions included 10 and 9 structural genes, respectively. A total of 177 bands were detected, of which 40.6% were variable. The proportion of variable bands in ctDNA (51.1%) was higher than that of mtDNA (28. 9%). The phylogenetic trees of plasmons, derived by two different models, indicate a common picture of plasmon divergence in the two genera and suggest three major groups of plasmons (Einkorn, Triticum, and Aegilops). Because of uniparental plasmon transmission, the maternal parents of all but one polyploid species were identified. Only one Aegilops species, Ae. speltoides, was included in the Triticum group, suggesting that this species is the plasmon and B and G genome donor of all polyploid wheats. ctDNA variations were more intimately correlated with vegetative characters, whereas mtDNA variations were more closely correlated with reproductive characters. Plasmon divergence among the diploids of the two genera largely paralleled genome divergence. The relative times of origin of the polyploid species were inferred from genetic distances from their putative maternal parents.

Variation in coxII intron in the wild ancestral species of wheat

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.