Assessing Loss of Regulatory Divergence, Genome–Transcriptome Incongruence, and Preferential Expression Switching in Abaca × Banana Backcrosses

The Musa textilis var. Abuab has high fiber quality (FQ) but is susceptible to abaca bunchy top virus (AbBTV); the Musa balbisiana var. Pacol has low FQ but is resistant against AbBTV. Their backcrosses (BC(2) and BC(3)) 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(2) and BC(3), respectively. Cis differences between the two genotypes are significantly reduced from BC(2) to BC(3) 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(3) relative to BC(2). 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(2) but switched to the Pacol- (or Abuab-) specific allele in the BC(3) genome.