title: Computation-assisted SiteFinding- PCR for isolating flanking sequence tags in rice.
abstract: SiteFinding-PCR is a method for isolating flanking sequence tags (FSTs) of T-DNA insertion lines, but the efficiency needs to be improved. Here we report a computation-assisted design for the random primers used in SiteFinding- PCR. A short sequence, GCATG, was screened from the rice genome and used as the 3' end of the random primer. When applying the optimized primer for isolating FSTs from 168 transgenic rice lines, we obtained 107 specific products, including 64 FSTs. The efficiency of obtaining FSTs using the modified version of SiteFinding-PCR increased by 73.0% compared with the method previously reported (P < 0.01, µ test). We also provide computational results for several other plant species such as maize, sorghum, Arabidopsis, foxtail millet, and Brachypodium based on the available genome data, so that the modified method could be easily adapted to other species.
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Hongru
authors.initials: H
authors.lastname: Wang
authors.forename: Jun
authors.initials: J
authors.lastname: Fang
authors.forename: Chengzheng
authors.initials: C
authors.lastname: Liang
authors.forename: Minghui
authors.initials: M
authors.lastname: He
authors.forename: Qiye
authors.initials: Q
authors.lastname: Li
authors.forename: Chengcai
authors.initials: C
authors.lastname: Chu
mesh_terms: D024509:3' Flanking Region; D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics*; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D030821:Plants, Genetically Modified; D016133:Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; C036483:T-DNA