Intergenic PCR for the S3-Haplotype Using S3-RNase and S3-SFB Specific Primers in Four Possible Combinations to Determine Distance between and Transcriptional Orientation of the Genes.
The primers used on genomic DNA are S3-RNase forward with S3-haplotype–specific SFB forward (A), S3-RNase forward with S3-haplotype–specific SFB reverse (B), S3-RNase reverse with S3-haplotype–specific SFB forward (C), and S3-RNase reverse with S3-haplotype–specific SFB reverse (D). Samples are as follows: ER, Early Rivers (S1S2); Col, Colney (S5S6); EF, Emperor Francis (S3S4); Nap, Napoleon (S3S4); 2434, JI 2434 (S3′S4); S3S3′ selection; water control. Only combination (A) shows specific amplification for accessions with the S3 allele.