Since the insertion sites of transposable elements are unique and often show high polymorphism even among wheat varieties, markers designed based on the repeat junction sites have also been termed "insertion site-based polymorphism (ISBP) markers.
For genotyping, simple sequence repeat (SSR) markers evenly distributed over the 12 chromosomes Temnykh et al. 2001; McCouch et al. 2002; International Rice Genome Sequencing Project 2005) and InDel markers designed based on the insertion-deletion polymorphism between YXZ and SBSM were used.
The STS markers schfc3 (designed based on the STS marker FC7[ 36]) and sts638[ 4], the Psy1-A1 marker csPSY[ 8] and five new markers (wri1, wri2, wri3, wri4 and wri5, Table 1) were assayed on Excalibur, Kukri and each of the 182 Excalibur/Kukri DH lines, using PCR conditions described in Additional file 5.
A 300-bp B1SM-F/B1SM-R SCAR marker was designed based on the sequence alignment of the B17 products.
A DNA marker was designed based on the mitochondrial cytochrome c oxidase subunit I gene, and fish species in surimi products were identified using a molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE); the results were subjected to sequence-based analysis.
The primer sequence of SCAR marker was designed based on the representative sequence for the cluster of these cultivar-specific insertion site (Supplementary Table S2).
The peroxisome marker was designed, based on the plant peroxisome targeting signal (PTS) [ 29, 39, 40], by fusing the PTS type 1 SKL to the C-terminus of the CFP (CFP-SKL).
The wx a -specific marker was designed based on the sequence of the insertion and amplifies a 615-bp fragment from the wx allele, whereas the wild-type allele-specific primer amplifies a 523-bp fragment from the non- waxy allele.
Simple sequence length polymorphism (SSLP) markers, similar to SSR markers, are designed based on a unique segment of genomic DNA sequence that contains a simple tandem repeat that distinguishes the genotypes.
Gene-based markers were designed based on intron sequences.
