With this approach, we found that the floral repressor VRN2 is present in many spring barleys, challenging its presumed role in determining winter growth habit. Interestingly, VRN1 expression also does not consistently associate with growth habit, pointing to a more complex regulatory network. 5/5

Therefore, misannotations need to be ruled out before claiming presence/absence variation or functional differences. This can be done by directly analyzing genome assemblies—going beyond simple motif searches or BLASTp analyses, which themselves rely on existing gene annotations. 4/5

Sampling different tissues AND considering circadian timing during harvest will capture more transcripts (e.g., ZT16 for HvCO1). This ensures annotations are based on evidence, not just prediction. 3/5

Why are gene annotations inconsistent across genotypes? Often, the reason isn’t a DNA difference but a lack of transcriptome data. This is especially critical for circadian-regulated genes such as HvCO1, which are mainly active in the evening. 2/5