Subgenome-informed statistical modeling of transcriptomes in 25 common wheat accessions reveals cis- and trans- regulation architectures

Common wheat is allohexaploid, where it is difficult to obtain homoeolog-distinguished transcriptome data. Lasy-Seq, a type of 3’ RNA-seq, is a technology efficient at obtaining homoeolog-distinguished transcriptomes. Here we applied Lasy-Seq to obtain transcriptome data from the seedlings, second leaves, and root tips of 25 common wheat lines mainly from East Asia. Roots and seedlings were similar to each other in transcriptome profiles, but they were different from the leaves. We then asked how three homoeologous genes from different subgenomes (i.e., triads) show different levels of expression. Specifically, we examined the effects of subgenomes, lines, and their interaction on the expression levels of each homoeolog triad, separately in each tissue. Of the 19,805 homoeolog triads, 51–55% showed significant effect of subgenome, suggesting cis-regulation, whereas 24–30% showed significant effect line, suggesting trans-regulation. We also found that 7.7–9.0% triads showed significant e..., This study obtained transcriptome data from seedlings, second leaves, and root tips of four replications of 25 NAM parental lines using Lasy-Seq. , , # Dataset: Subgenome-informed statistical modeling of transcriptomes in 25 common wheat accessions reveals cis- and trans- regulation architectures

[https://doi.org/10.5061/dryad.fqz612jzq](https://doi.org/10.5061/dryad.fqz612jzq)

This study obtained transcriptome data from seedlings, second leaves, and root tips of four replications of 25 NAM parental lines using Lasy-Seq. Roots and seedlings were similar transcriptome profiles to each other and different from leaves. We determined the effects of subgenomes, lines, and their interactions by leaves, roots and seedlings on expression levels for each homoeolog triads. Of the 19,805 homoeolog triads, the percentages of homoeolog triads with significant subgenome, line and interaction effects were 50.9–55.4%, 24.2–29.5% and 7.7–9.0%, respectively. GO term enrichment analysis showed that GO terms related to each tissue type function were enriched in expressed genes in leaves and roots.

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