Switches in homoeolog expression bias in hexaploid wheat are associated with cis-variation

Differences in the relative level of expression of homoeologs, known as homoeolog expression bias (HEB), is widely observed in allopolyploids. 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.Here we use biparental mapping populations of hexaploid wheat with a common Paragon parent to explore the inheritance of homoeolog expression bias in the F6 generation.We found that homoeolog expression bias is inherited for 26-27% of triads. Most triads conserved a similar homoeolog expression bias pattern as one or both parents. Inherited patterns were largely driven by changes in the expression of one homoeolog, allowing homoeolog expression bias in subsequent generations to match parental expression, and produce a switching between homoeolog expression bias profiles. Novel patterns of homoeolog expression bias occurred more frequently in the biparental population from a landrace x elite cross, than in the population with two elite parents.These results demonstrate that there is significant reprogramming and stabilisation of homoeolog expression bias within a small number of generations that differs significantly based on the parental lines used in the crossing.

部分同源基因（homoeolog）的相对表达水平差异，即部分同源基因表达偏倚（homoeolog expression bias, HEB），在异源多倍体中广泛存在。尽管通过杂交介导的部分同源基因表达偏倚演化过程已得到系统解析，但在较短时间尺度下，多代间部分同源基因表达偏倚的保留或改变程度仍不甚明晰。本研究以携带共同亲本Paragon的六倍体小麦双亲作图群体为实验材料，探究F6代中部分同源基因表达偏倚的遗传规律。研究发现，26%-27%的三联体基因座（triads）的部分同源基因表达偏倚可遗传。多数三联体基因座保留了与其中一个或两个亲本一致的部分同源基因表达偏倚模式。可遗传的表达偏倚模式主要由单个部分同源基因的表达变化驱动，使得后续世代的部分同源基因表达偏倚可匹配亲本的表达特征，并可在不同的部分同源基因表达偏倚谱间发生切换。相较于由两个优良亲本构建的作图群体，来自地方品种与优良品种杂交组合的双亲群体中，新型部分同源基因表达偏倚模式的出现频率更高。上述结果表明，仅经数代繁殖，部分同源基因表达偏倚即可发生显著的重编程与稳定化，且该过程因杂交所用亲本组合的不同而存在显著差异。