Philippa.Borrill@jic.ac.uk

Differences in the relative level of expression of homoeologs, known as homoeolog expression bias (HEB), is widely observed in allopolyploids including wheat. While the evolution of homoeolog expression bias through hybridisation has been characterised, on shorter timescales the extent to which homoeolog expression bias is preserved or altered between generations remains elusive. In wheat breeding programmes, these inter-generational changes in homoeolog expression bias may influence significant traits including flowering time and spike development.

Using two biparental mapping populations consisting of 50 F6 lines we identified over 5,000 triads exhibiting substantial variation in HEB. We measured the relative distance between HEB of F6 lines and their parents in these 5,000 triads. One cross exhibited a higher prevalence of triads with notably divergent HEB from a single parent, whereas the other cross predominantly displayed divergence from both parents. To understand, if these trends are associated with genetic variation between the parental wheat varieties, we performed variant calling and discovered over 80,000 SNPs.

These SNPs revealed direct associations with HEB in 800 triads and cis- variation was strongly associated with switches in HEB between F6 lines. Furthermore, we investigated whether there are specific genomic loci that contribute to this inheritance. eQTL analysis of more than 200 F6 lines, revealed over 7,000 cis- and 2,000 trans- loci that likely contribute to the inheritance of HEB in wheat. Notably, 95 of these eQTL loci were shared across F6 lines derived from distinct biparental crosses, indicating a common genetic framework influencing HEB across populations.

Our study highlights that homoeolog expression bias is heritable and can alter rapidly within a few generations, and this may contribute variation within wheat breeding programmes.