For understanding the genetic diversity and genetic relationship between cultivated and weedy types, we evaluated genetic variation of 80 accessions of rice (O. Sativa). This included 42 cultivated accessions and 38 weedy accessions with the help of AFLP and CACTA-TD. A total of 542 loci were analyzed (255 for AFLP and 287 for CACTA-TD) of which AFLP markers exhibited 75% of polymorphism and transposon based CACTA-TD markers exhibited 93% of polymorphism. The average genetic diversity value for all 80 accessions, using AFLP markers was 0.226 (Cultivated – 0.210; Weedy 0.241) and based on CACTA-TD markers was 0.281 (Cultivated – 0.294; Weedy 0.269). A UPGMA phylogenetic tree revealed three major groups for both the marker system. The average polymorphic content value obtained with AFLP and CACTA-TD markers were 0.21 and 0.232, Effective multiplex ratio (AFLP – 47.50; CACTA-TD – 66.75), Marker Index (AFLP – 9.94; CACTA-TD – 21.13) and Resolving power (AFLP – 19.53; CACTA-TD – 34.62) indicated that the CACTA-TD markers were relatively efficient than AFLP markers.

Transposon elements are widely distributed in the plant genomes. Maize genome consists of various transposable elements that constitute as much as 80% of the genome. Transposon display (TD) is a modified from AFLP, and can be used to generate and display hundreds of genomic fragments affixed to transposons, consequently tagging transposons. We developed maize specific transposon insertion- sequence characterized amplified regions (Ti-SCAR) using Isaac and CACTA transposons. Currently, we have developed 58 dominant Ti-SCAR markers. Validation of the Ti-SCARs is being carried out using a various maize germplasm. Since AFLP is tedious and unsuitable for large scale application in MAS, the Ti-SCAR markers displayed simple binary presence or absence pattern. Thus, the Ti-SCARs can provide a fast, cheap and reliable PCR based assay. A pipeline in developing the Ti-SCAR will be presented in the poster.

EST-SSRs were developed in Brassica napus by database mining. We isolated 7,802 EST-SSRs from the B. napus 643,946 ESTs deposited in the NCBI. With the cut-off value of >10 repeats in di-nucleotide repeats and >7 tri-nucleotide repeats, 303 ESTs were suitable for primer designing for PCR amplification. Of the sixteen possible di-nucleotide combinations, only three types of repeats (AC/GT, AG/CT, and AT/TA) were present among the di-nucleotide EST-SSRs. Whereas, 27 tri-nucleotide repeat motifs from the 64 possible combinations were present. The repeat numbers ranged from 10-15 in di-nucleotide repeats and 7-9 in tri-nucleotide repeat motifs, respectively. By checking PCR amplification in 10 Korean rapeseed breeding lines or cultivars, 234 primer pairs showed successful PCR amplification and 142 of the 234 primer pairs revealed polymorphism among the control cultivars or breeding lines. While the repeat length does not related with the SSR polymorphisms, the repeat motif number showed positive relation with the polymorphism generation by showing higher repeat numbers with higher polymorphisms. We are here presenting the PCR amplifiable primer sequences of the 234 SSR primer pairs to aid in the germplasm management and breeding programs of the B. napus in Korea.