Abstract:Simple Sequence Repeats (SSR) were surveyed in citrus BACEnd sequence (BES) for the development of new SSR markers to extend and saturate existing genetic map.22 403 SSRs with 1~6 bp motif were identified in 46 339 citrus BESs retrieved from NCBI.The estimated frequency of SSRs was approximately 1/1.25 kb,nearly twice the frequency found in Citrus Expressed Sequence Tags.323 primers were selected in the present mapping study,of which 40 were mononucleotide repeats,184 dinucleotide repeats,99 trinucleotide or above repeats.Polymorphism tests showed that 316 primerpairs (98%) could be amplified successfully and 173 pairs (55%) were polymorphic.Among the polymorphic primers,15 pairs were of mononucleotide repeats,100 pairs of dinucleotide repeats,58 pairs of trinucleotide or above repeats.A new linkage map was produced by combining the segregating data of new markers and markers in the previous map.When compared with the published map,the new map integrated 334 SSR markers,9 linkage groups and covered 844.2 cM of citrus genome with an average genetic distance standing at 2.53 cM.The results demonstrated that citrus BES was good for SSR marker development and the developed markers were useful in extending and saturating the citrus genetic maps.So this will provide a reference for development of other species SSR markers and lay a good foundation for citrus gene mapping,mapbased cloning and markerassisted breeding.