Identification of hypervariable chloroplast intergenic sequences in onion (Allium cepa L.) and their use in analysing the origins of male sterile onion cytotypes.

摘要

To study the phylogeny of onion (Allium cepa L.) cytotypes, and closely-related Allium species, polymorphisms in chloroplast intergenic sequences were searched among seven distantly-related Allium species. The percentage of variable nucleotides in the intergenic sequences between rps16 and trnQ was approx. five-fold higher than that in other non-coding regions. A phylogenetic tree of 35 Allium species, including three onion cytotypes, was constructed using hypervariable chloroplast DNA sequences between rps16 and trnQ. Phylogenetic analysis revealed that A. vavilovii and A. dictyoprasum were close relatives of the normal and cytoplasmic male sterile (CMS)-T cytotypes of onion, and that the sequences of the normal and CMS-T cytotypes were identical, supporting the recent autoplasmic origin of CMS-T male-sterility from the normal cytotype. Conversely, the CMS-S cytotype was closely-related to A. galanthum and A. roylei, supporting the alloplasmic origin of CMS-S male sterility. A variant of the hypervariable rps16-trnQ sequence containing a single nucleotide polymorphism and a 4-bp deletion compared to the normal cytotype, was identified in the onion germplasm studied, and a molecular marker was developed to detect the variant chlorotype. PCR amplification profiles of the different mitochondrial genome organisations showed that the new chlorotype may have been derived from the normal cytotype.