Expression‐level support for gene dosage sensitivity in three Glycine subgenus Glycine polyploids and their diploid progenitors

Abstract

Retention or loss of paralogs following duplication correlates strongly with the function of the gene and whether the gene was duplicated by whole-genome duplication (WGD) or by small-scale duplication. Selection on relative gene dosage (to maintain proper stoichiometry among interacting proteins) has been invoked to explain these patterns of duplicate gene retention and loss. In order for gene dosage to be visible to natural selection, there must necessarily be a correlation between gene copy number and gene expression level (transcript abundance), but this has rarely been examined. We used RNA-Seq data from seven Glycine subgenus Glycine species (three recently formed allotetraploids and their four diploid progenitors) to determine if expression patterns and gene dosage responses at the level of transcription are consistent with selection on relative gene dosage. As predicted, metabolic pathways and gene ontologies that are putatively dosage-sensitive based on duplication history exhibited reduced expression variance across species, and more coordinated expression responses to recent WGD, relative to putatively dosage-insensitive networks. We conclude that selection on relative dosage has played an important role in shaping gene networks in Glycine.

Foreign cry1Ac gene integration and endogenous borer stress-related genes synergistically improve insect resistance in sugarcane

“…However, for Group II (ROC22 background), no obvious linear relationship was observed. For Group II, our findings are inconsistent with the dosage effect theory or the GBH theory, which suggests that the greater the transgene copy number, the higher its expression level [22, 55, 56]. Transgene copies can greatly affect expression levels [55, 56].…”

“…The gene balance hypothesis suggests that increasing the transgene copy number would upregulate gene expression levels, and thus a correlation (positive or negative) must exist between gene copy number and gene expression level [22]. Therefore, transcript abundance must increase with gene dosage in order to increase protein abundance [22]. However, low copy-number exogenous genes are considered to be beneficial for plant improvement, particularly in diploid plants [21].…”

Genomic analysis reveals major determinants ofcis-regulatory variation inCapsella grandiflora

“…Finally, defense-related genes, which are thought to be dosage-insensitive in plants (40), were significantly enriched among genes with cis-regulatory variation in our study, whereas protein-binding genes were nominally enriched among control genes without ASE. Both promoter polymorphism and TE insertions, which can impact expression in several ways (41), might be more likely to be tolerated near dosage-insensitive genes.…”

Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies

“…). The most studied is G. dolichocarpa T2 (Coate et al, ; Coate et al, ; Coate et al, ; Coate et al, ; Powell & Doyle, ). The other two, G. tomentella s.l.…”