[Data mining for SSRs in ESTs and development of EST-SSR marker in oilseed rape].
Totally 2803 SSRs distributed in 2443 ESTs were mined out and accounted for 13.58% of 17987 non-redundant ESTs from oilseeed rape, with the average distance of distribution about 4.26 kb. Dinucleotide and trinucleotide repeats are the dominant type, with similar frequency and accounting for 89.05% together in all SSRs. AG/CT and AAG/CTT are the most frequent motifs, accounting for 84.31% and 37.71% in dinucleotide and trinucleotide repeats respectively. Further, 23 primer pairs for EST-SSRs were designed and the suitable annealing temperature for each primer pair was determined by gradient PCR. The amplification and polymorphism displayed by these primers in 10 varieties of oilseed rape were detected by using silver staining of nondenaturing polyacrylamide gel. 21 primer pairs showed the amplification, accounting for 91.30% of total primers, and 12 primer sets showed polymorphisms, accounting for 57.14% of primers available. These results indicate that it is an effective and feasible approach to develop SSR markers based on ESTs in oilseed rape.
Li
Xiao Bai
XB
Institute of Nuclear and Agricultural Sciences, Zhejiang University, Hangzhou 310029, China.
Zhang
Ming Long
ML
Cui
Hai Rui
HR
D015415:Biomarkers; D029688:Brassica napus / Q000235:genetics*; D017931:DNA Primers; D018744:DNA, Plant / Q000032:analysis; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D018745:Genome, Plant / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics; D018598:Minisatellite Repeats; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic
D015415:Biomarkers; D017931:DNA Primers; D018744:DNA, Plant