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

Ereful, Nelzo C.; Lalusin, Antonio G.; Laurena, Antonio C.

doi:10.3390/genes13030519

Cited by 6 publications

(12 citation statements)

References 45 publications

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“…Based on initial field assessment, it has superior fiber quality and is resistant against bunchy top virus. Molecular study using RNA-seq revealed that it is the best among five abaca genotypes as it induces significantly higher number of genes associated with both desirable traits [16].…”

Section: Resultsmentioning

confidence: 99%

“…Only features with total normalized read count of 20 reads between the two specific alleles were considered for further analysis (AbuabBC2 + PacolBC2 ≥ 20; AbuabBC3 + PacolBC3 ≥ 20) to ensure genes are expressed and to avoid inclusion of artifacts, as previously performed (e.g. [12,16,37,38]. We incremented read counts with a value of 1 for genotype-specific alleles with 0 read counts to avoid a numerator or a denominator of 0.…”

Section: Allelic Imbalance Polymorphism In the Backcrossesmentioning

confidence: 99%

“…The genome-wide expression performance of the abaca-specific genes of BC2 and BC3 along with their parents were shown in a companion paper [16]. However, assessment of regulatory divergence between the parents and asymmetric expression in their backcrosses has not been performed.…”

Section: Regulatory Divergence Between Abuab and Pacolmentioning

confidence: 99%

“…As polysaccharide and lignin were found associated with high-fiber quality [16], we searched for such genes allelically imbalanced in BC2. We found 16 genes encoding for either putative cellulose synthase or cellulose synthase, 14 of which preferred the Abuabspecific allele (|Log2FC|≥1; FDR<0.05).…”

Section: Allelic Imbalance In the Bc2 Genomementioning

confidence: 99%

“…ASE has been a subject of a number of papers in different organisms such as humans [8,9], Drosophila [10,11,12], maize [13], stickleback [14], coffee [15], and rice [16,17]. There are several approaches in assessing ASE which include single-base extension [18], pyrosequencing [10], and most recently RNA-seq (e.g.…”

Section: Introductionmentioning

confidence: 99%

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

Ereful¹,

Lalusin²,

Laurena³

2022

Preprint

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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.

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Section: Resultsmentioning

confidence: 99%