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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #120108
Title: SEQUENCE ANALYSIS OF A CHLOROPLAST INTERGENIC SPACER FOR PHYLOGENETIC ESTIMATES IN ALLIUM SECTION CEPA AND A PCR-BASED POLYMORPHISM DETECTING MIXTURES OF MALE-FERTILE AND MALE-STERILE CYTOPLASMIC ONION

Author
item LILLY, JASON - DEPT HORT UW MADISON WI
item Havey, Michael

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/28/2001
Publication Date: N/A
Citation: N/A

Interpretive Summary: We studied diversity at a specific region of the chloroplast DNAs of onion and its closest relatives. The relationships among these plant species estimated by differences in this specific region were similar, but not identical to, the relationships estimated using the entire chloroplast DNA. Differences were likely due to mistakes during DNA replication. A specific difference in the DNA was discovered between normal (N) male-fertile and male-sterile (S) cytoplasms of onion. S cytoplasm conditions male sterility and allows the production of hybrid onion seed. Occasionally, there are seed mixtures or harvesting errors that occur during hybrid-onion seed production. We used the difference between N and S cytoplasms to develop a molecular marker revealing very low amounts of N cytoplasm in hybrid seed lots. The contaminating N cytoplasm would most likely be due to seed mixtures during harvest. This marker can be used by seed companies in the quality control of hybrid-onion seed to identify and eliminate mixtures involving the male parent of the hybrid.

Technical Abstract: Restriction-enzyme analysis of the chloroplast (cp) DNA yielded maternal phylogenies supporting a close phylogenetic relationship among normal (N) male-fertile and male-sterile (S) cytoplasmic bulb onion (Allium cepa), A. altaicum, A. fistulosum, A. galanthum, A. roylei, and A. vavilovii. S cytoplasm of onion is likely an alien cytoplasm introduced in antiquity into onion populations. We previously showed that size differences in an intergenic spacer in the cp DNA distinguish N and S cytoplasms of onion. We cloned and sequenced this intergenic spacer from N and S cytoplasms of onion, A. altaicum, A. fistulosum, A. galanthum, A. pskemense, A. oschaninii, A. roylei, and A. ampeloprasm (outgroup) to identify the nature of previously described RFLPs and to develop a PCR-based marker revealing N-cytoplasmic contamination of S-cytoplasmic hybrid seed lots. Phylogenies based on restriction-enzyme analysis of the entire cp DNA were similar, but not identical, to those based on sequence divergence in this intergenic region.