RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (Musa textilis Nee)

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 (BC₂ and BC₃) 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 BC₂ and BC₃, respectively. Cis differences between the two genotypes are significantly reduced from BC₂ to BC₃ 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 BC₃ relative to BC₂. 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 BC₂ but switched to the Pacol- (or Abuab-) specific allele in the BC₃ genome.