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

Nelzo C Ereful; Antonio G Lalusin; Antonio C Laurena

doi:10.3390/genes13081396

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

Genes (Basel). 2022 Aug 6;13(8):1396. doi: 10.3390/genes13081396.

Authors

Nelzo C Ereful^{1

2}, Antonio G Lalusin³, Antonio C Laurena²

Affiliations

¹ Biochemistry Laboratory-Plant Physiology Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, Laguna 4031, Philippines.
² Philippine Genome Center for Agriculture, University of the Philippines Los Baños, Laguna 4031, Philippines.
³ Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, Laguna 4031, Philippines.

Abstract

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.

Keywords: abaca (M. textilis); allele-specific expression; allelic imbalance; banana (M. balbisiana); regulatory divergence.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
Musa* / genetics
Transcriptome / genetics

Grants and funding

This project has been supported by the Abaca Genomics project (N9-197-21) and Balik Scientist Program (N601600 and N602000), both funded by DOST–PCAARRD. Likewise, the APC was funded by DOST–PCAARRD.