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Title: EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata

item Bowman, Kim
item CHOI, YOUNG - University Of Florida
item Dang, Phat
item RAO, MADHUGIRI - University Of Florida
item SONEJI, JAYA - University Of Florida
item McCollum, Thomas
item GMITTER, JR, FRED - University Of Florida

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/21/2007
Publication Date: 2/23/2007
Citation: Chen, C., Bowman, K.D., Choi, Y.A., Dang, P.M., Rao, M., Huang, S., Soneji, J.R., Mccollum, T.G., Gmitter, Jr, F.G. 2007. EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata. Tree Genetics and Genomes. 4:1-10. 2008.

Interpretive Summary: Simple sequence repeats (SSR) are short tandem repeats in DNA sequence that are useful as genetic markers. Expressed sequence tags (ESTs) represent actual genes that are expressed in the plant. These EST-SSR markers can be used in the development of genetic linkage maps, which can be integrated with physical maps of DNA. Physical maps are essential for understanding how genes for a species are organized on chromosomes. We studied the segregation of 141 EST-SSR markers in a population of citrus hybrids that was generated by crossing sweet orange with Poncirus trifoliata (a citrus relative useful in citrus breeding). Results obtained were used to develop linkage maps which identify the location of specific genes on specific chromosomes. Such maps are important tools for plant breeders and molecular biologists who are working to develop improved varieties of citrus. All SSR primers developed in this project are freely available to the citrus research community. Results of this work will aid in understanding taxonomic relationships among different types of citrus, as well as the development of improved citrus cultivars.

Technical Abstract: The segregation of 141 polymorphic EST-SSR (expressed sequence tag - simple sequence repeat) markers in an F1 intergeneric citrus population was studied to build the first extensive EST maps for the maternal sweet orange and paternal Poncirus genomes. Of these markers, 122 were found segregating in sweet orange, 59 in Poncirus, and 40 in both. Eleven linkage groups with 113 markers in sweet orange, eight with 45 markers in Poncirus, and thirteen with 123 markers in the CP (Cross Pollinator) consensus of both, were constructed. About 775.8cM of sweet orange genome and 425.7cM of Poncirus genome were covered. Through comparison of shared markers, three cases were found where two linkage groups in one map apparently were colinear with one group from the other map; Poncirus linkages Ar1a and Ar1b, and consensus linkages CP1a and CP1b, were both collinear with one sweet orange linkage, Sa1, as were sweet orange Sa3a and Sa3b with Poncirus Ar3 and consensus CP3, and sweet orange Sa7a and Sa7b, and consensus CP7a and CP7b with Poncirus Ar7. These EST-SSR markers are particularly useful for constructing comparative framework maps for different related genera, because they amplify closely related genes to provide anchor points across taxa. The putative functions of some of these mapped ESTs were also predicted. All SSR primers are freely available to the citrus community.