Quantification of total and allelic expression.

(A) Common and allele-specific primers were designed for quantification of total and allelic expressions in a target gene. In each allele-specific primer, Single nucleotide polymorphisms (SNPs), insertions, deletions (InDel) or substitutions were placed at the 3′ ends of primers and the second base from the 3′ end of each primer was substituted to be a mismatch nucleotide for discrimination of Hd-rR and HNI transcripts. Use of the three types of primers enabled comparisons of allele-specific expression in reciprocal hybrids. (B) Allelic expression (A′ or B′) in hybrid were calculated using correction factors, α and β, for each allele-specific primer (see ‘Materials and Methods’ section). These factors were determined from ratio of total expressions (e.g. Hd-rR(Cp) and Hd-rR(AS(d))) quantified by common and allele-specific primers in each parental strain. Cp: common primer. AS(d) and AS(N): allele-specific primer for Hd-rR or HNI allele. α and β: the ratio of total expressions of common and allele-specific primers.