Despite the importance of and current demand for abaca (Musa textilis Nee) fiber, there has been limited study that capitalizes on RNA-seq to identify candidate genes associated with high fiber quality and bunchy top virus (AbBTV) resistance. Three varieties (Abuab, Inosa, and Tangongon), one wild banana variety (Musa balbisiana Colla) Pacol, and two developed backcrosses (Abuab × Pacol BC₂ and BC₃) were grown at the Institute of Plant Breeding (IPB), Laguna, Philippines. The pseudostems of 3-month-old suckers of each genotype were sampled for RNA-seq. Datasets were analyzed for differential expression (DE) implementing various model frameworks, including pairwise, genotypic and non-DE models. Results indicate that Abuab and BC₃ induce the highest proportion (70%) of abaca-specific genes. Gene ontology (GO) enrichment analysis showed several genes associated with cellulose synthase activity, callose synthase, ß-glucosidase activity, glucan biosynthetic process, etc. KEGG pathway analysis showed several genes encoding for enzymes involved in the lignin biosynthetic pathway. Analysis using genotypic DE (GDE) between abaca bunchy top virus (AbBTV)-resistant and -susceptible groups revealed genes such as pathogenesis-related protein and NBS-LRR. As the genotypes were not infected with the pathogen, these genes are yet to be confirmed for their roles in disease resistance and are an interesting subject for further investigation.

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.

The Musa textilis var. Abuab has high fiber quality (FQ) but has low resistance against abaca bunchy top virus (AbBTV); the Musa balbisiana var. Pacol, has low FQ but high resistance 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 the 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 which we refer here as “genome–transcriptome incongruence”. We also observed preferential expression switching in which several genes prefer Abuab- (or Pacol-) specific allele in the BC2 but switched to Pacol- (or Abuab-) specific allele in the BC3 genome.

The genetic and phenotypic diversity of sweet potato (Ipomoea batatas L. Lam) germplasm collected from Luzon, Philippines, was assessed through integrated morphological and molecular approaches. A total of 264 accessions, including released varieties, advanced lines, and hybrids, were characterized. Morphological evaluation revealed distinct variability in vegetative and storage root traits. Leaf morphology ranged from triangular to semi-elliptical with pigmentation varying from green to purple, while lobe number reflected high phenotypic plasticity. Storage roots exhibited diverse shapes, from elliptic to oblong, and variable pigmentation (orange to purple), indicative of carotenoid and anthocyanin accumulation. Environmental conditions, particularly excessive soil moisture, influenced trait expression by reducing pigmentation intensity and inducing structural deformities such as grooves and constrictions. Phenotypic diversity analysis using the Shannon Diversity Index revealed high variability in vine pubescence and skin pigmentation (H′ ≥ 0.67) but limited diversity in mature leaf color and flesh pigmentation (H′ ≤ 0.33). Cluster analysis (UPGMA) grouped the genotypes into 10 clusters, reflecting both genetic variation and environmental effects. Complementary molecular characterization using 54 SSR primers, of which 33 were polymorphic, confirmed substantial allelic diversity. The mean polymorphic information content (PIC) was 0.909, demonstrating strong discriminatory power. SSR-based clustering grouped 156 genotypes into 12 clusters at a Jaccard similarity coefficient of 0.89, providing higher resolution than morphological analysis and delineating regional populations and hybrid groups. The integration of phenotypic and molecular data highlights the extensive diversity within Philippine sweetpotato germplasm. While morphological traits were environmentally influenced, SSR markers effectively resolved genetic relationships and population structure. This combined framework provided a robust basis for germplasm management and utilization. The findings underscored the importance of conserving diverse alleles and exploiting them for breeding programs focused on pigmentation, root quality, stress resilience, and yield improvement, thereby supporting sustainable sweet potato production in the Philippines.