| Summary: | The <i>Musa textilis</i> var. Abuab has high fiber quality (FQ) but is susceptible to abaca bunchy top virus (AbBTV); the <i>Musa balbisiana</i> var. Pacol has low FQ but is resistant against AbBTV. Their backcrosses (BC<sub>2</sub> and BC<sub>3</sub>) possess both desirable traits. Analysis using RNA-seq showed that the regulatory divergence of Abuab and Pacol is largely explained by cis differences with 27.4% and 22.3% if we are to assess it using BC<sub>2</sub> and BC<sub>3</sub>, respectively. Cis differences between the two genotypes are significantly reduced from BC<sub>2</sub> to BC<sub>3</sub> due to changes in genomic constitution. Trans, on the other hand, is robust to changes in allelic composition. All these are attributed to the loss of heterozygosity in BC<sub>3</sub> relative to BC<sub>2</sub>. Further analysis showed that both backcrosses exhibited genome-wide preferential expression of Pacol- over Abuab-specific alleles, despite the wider genetic presence of the latter in the hybrids. The ratio of the two genotype-specific expressed transcripts and the ratio of their corresponding genetic make-up are significantly disproportionate, a phenomenon that we refer to here as “genome–transcriptome incongruence”. We also observed preferential expression switching in which several genes prefer the Abuab- (or Pacol-) specific allele in BC<sub>2</sub> but switched to the Pacol- (or Abuab-) specific allele in the BC<sub>3</sub> genome.
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