title: Single- and double-SSR primer  combined analyses in rice.
abstract: Polymerase  chain reaction (PCR) is the foundation of SSR molecular marker technology. We  used sib rice varieties J518, XD1 and SD23 as experimental materials, selecting  30 pairs of SSR primers, including RM127, RM337 and RM5172, covering the rice  genome, and performed single- and double-SSR primer combined analyses. We found  that under the same PCR system and conditions, a single primer of the SSR  primer pairs could amplify the same fragments as double primers do. The  sequencing results demonstrated that some amplified fragments that we  previously believed to come from double primers were actually produced by a  single primer. The use of this kind of primer, such as the RM127 primer pair,  for marker-assisted breeding will therefore be misleading. Additionally, using  the same PCR system and conditions, some single primers that are part of SSR  primer pairs can amplify many more specific fragments than double-SSR primers.  For instance, in the case of the RM5172 primer pair, a single primer P1  amplified approximately three times the number of fragments as the double  primer. This information can contribute to research on genetic diversity of  species, understanding of genetic relationships and identification of germplasm  resources. Accordingly, combined analyses of single- and double-primer  amplification products not only can remove single-primer amplification  fragments and false-positives from double-primer amplification products in  order to improve test accuracy, but also can facilitate research on genetic  diversity, exploration of phylogenetic relationships and identification of  germplasm resources. We define this method as "single- and double-SSR primer  combined analyses".
authors.affiliation: Biotechnology Center of Jilin Agricultural University, Changchun, China.
authors.forename: J
authors.initials: J
authors.lastname: Ma
authors.forename: S C
authors.initials: SC
authors.lastname: Guan
authors.forename: Z
authors.initials: Z
authors.lastname: Zhang
authors.forename: P W
authors.initials: PW
authors.lastname: Wang
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D012275:Oryza / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods*; D011110:Polymorphism, Genetic
chemical_list: D017931:DNA Primers