Poster: Genomics Resources

Abs # 936: Development of PCR-based markers for genetic mapping based on BAC-end sequence and ESTs in Chinese cabbage

Presenter:	Lim, Yong Pyo , yplim@cnu.ac.kr
Authors	Lim, Yong Pyo  (A)   Choi, Su Ryun  (A)   Cui, Harui  (A)   Woo, Seung Min  (B)   Choi, Kwan Sam  (B)
Affiliations:	(A): Department of Horticulture and Genome Research Center (B): Division of Applied Biology and Chemistry, and Genome Research Center

It was developed the co-dominant polymorphic markers based on the BAC-end sequences and expressed sequence tags. SSR markers were developed using the known BAC-end sequence information. Out of 2,376 BAC-end sequencing data, we found 58 clones containing repeat motif using Repeatmasker program, and designed 41 primer pairs with Primer 3 software. Thirteen pairs out of 41 designed primer allow the polymorphism as SSR marker in Brassica rapa. EST markers were developed based on 1,736 ESTs. Some ESTs were selected to design primers for PCR. One hundred and fifty pairs of primers to specific ESTs have been designed. The amplified products were separated by 1.2-3.0% agarose gel to check polymorphism, such as obvious differences in band number or band size between the parents used to construct DH population. If no variation were observed, the differences of PCR products in pattern of restriction digestion would be further checked. Based on the band pattern, genotype of each DH line was determined. To date, about 23.3% of primers showed the polymorphism among the parents and 89 DH lines. We also found that the amplified segment containing the intron(s) was more polymorphic.