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With respect to xa5, a multiplex-PCR based functional marker system, named xa5FM, consisting of two sets of primer pairs targeting the 2-bp functional nucleotide polymorphism in the exon II of the gene TFIIAɤ5 (candidate for xa5), has been developed.
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This system, named CPS-SLAM, consists of a parent robot with a 3D laser scanner and child robots with target markers.
Another high-throughput system, named Sequenom iPLEX Gold genotyping technology provides an ideal technique for medium sized projects, when scoring between 5 and 400 SNP markers on hundreds to a few thousands of DNA samples [ 23].
We adopted the scoring system named CHS proposed by Huffman.
Saikko et al. developed a test system named Random POD.
Using an active marker system helped us get a clean capture.
For HWA1 mapping, a total of 83 DNA markers distributed on the whole rice genome were used: 24 polymorphic indel markers in Fig. 2, an indel marker named S21074 designed by RGP, another indel marker named Knindel1 (Matsubara et al. 2007), a sequence characterized amplified region (SCAR) marker named d (Ueda et al. 2005), and 56 published SSR markers.
The SCAR marker was named SCA50.
Table S3 (Additional File 13) provides a cross-reference between synonymous marker names, relating SNPs mapped in the present work to the same genes mapped previously using other marker systems [ 3].
Additionally, compared with other marker systems, SSR-based assays are labour-intensive and time-consuming.
Find the system name.
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