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United States Department of Agriculture

Agricultural Research Service

Title: Genetic Mapping of Expressed Sequences in Onion and in Silico Comparisons with Rice Show Scant Colinearity

Authors
item Martin, William - BALL SEED CO CHICAGO IL
item Mccallum, John - CROP & ROOD R NEW ZEALAND
item Shigyo, Masayoshi - YAMAGUCHI UNIV JAPAN
item Jakse, Jernej - UNIV OF WISCONSIN
item Kuhl, Joseph - MICHIGAN STATE UNIV
item Yamane, Naoko - YAMAGUCHI UNIV JAPAN
item Pither-Joyce, Meeghan - CROP & FOOD R NEW ZEALAND
item Gokce, Ali Fuat - ULUDAG UNIV TURKEY
item Sink, Kenneth - MICHIGAN STATE UNIV
item Town, Christopher - THE INST FOR GEN RES MD
item Havey, Michael

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 12, 2005
Publication Date: July 15, 2005
Citation: Martin, W.J., Mccallum, J., Shigyo, M., Jakse, J., Kuhl, J.C., Yamane, N., Pither-Joyce, M., Gokce, A., Sink, K.C., Town, C.D., Havey, M.J. 2005. Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity. Molecular Genetics and Genomics. 274:197-204.

Interpretive Summary: The plant orders Poales (includes the grasses) and Asparagales [includes onion (Allium cepa L.) and other Alliums] are two of the most economically important groups. Enormous genetic resources, such as DNA sequences, have been developed for the grasses, however their applicability to other major groups, such as the Asparagales, is unclear. Expressed regions of the onion DNA (ESTs) were selected that showed significant similarities to single positions in the rice DNA. One hundred new genetic markers developed from these ESTs were added to genetic map of onion and genetic linkage groups were assigned to chromosomes. Visual inspections of genetic linkages in onion with physical linkages in rice revealed scant colinearity. These results demonstrate that the grasses are not appropriate genetic models for other important monocots such as onion, requiring the identification and development of models for the Alliums and other important plants in the Asparagales. These results will be useful for plant breeders and geneticists working on important monocot plants outside of the grasses.

Technical Abstract: The Poales (includes the grasses) and Asparagales [includes onion (Allium cepa L.) and other Alliums] are the two most economically important monocot orders. Enormous genomic resources have been developed for the grasses, however their applicability to other major monocot groups, such as the Asparagales, is unclear. Expressed sequence tags (ESTs) of onion (Allium cepa L.) were selected that showed significant similarities (80% similarity over at least 70% of the sequence) to single positions in the rice genome. One hundred new genetic markers developed from these ESTs were added to the intraspecific map from the BYG15-23 by AC43 segregating family, producing 10 linkage groups encompassing 1907 cM at LOD 4. Onion linkage groups were assigned to chromosomes using alien addition lines of Allium fistulosum L. carrying single onion chromosomes. Visual comparisons of genetic linkages in onion with physical linkages in rice revealed scant colinearity, although short regions of colinearity were observed. Our results demonstrate that the grasses may not be appropriate genomic models for other monocots such as onion, requiring the identification and development of genomic models for the Alliums and other important plants in the Asparagales.

Last Modified: 11/24/2014
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