The object of this study was to use genomic information obtained from wheat-rice sequence to develop genome-specific PCR primer for Agp-L gene involved in starch biosynthesis. Intron locations in wheat were inferred through alignment of wheat cDNA sequence of Agp-L with rice genomic sequence. Exon-anchored primer which amplify across introns allowed sequencing of introns from the three genomes provided the basis for genome-specific primer design. The single nucleotide polymorphism (SNP) was identified and this SNP could be converted into cleaved amplified polymorphism sequence (CAPS).

To facilitate breeding of lines with either the Ppd-D1a or ppd-d1a, we screened 342 F2 progenies from a cross between Laura (photoperiod insensitive, Ppd-D1a) spring wheat and SWP5304 (photoperiod sensitive, ppd-d1a) for their time to heading under 10 hour day length, and with a set of 37 microsatellite primers previously mapped to chromosome 2D. Bulk segregant analysis was used to identify tow linked microsatellite loci. The Ppd-D1a locus was flanked by Xgwm484 with 13.7 cM distance and Xgwm455 with 27 cM. These markers may be useful in selection of the desired photoperiod sensitivity in segregating populations grown in Northern latitude.