The genetic distance between hybridizing parents affects heterosis; however, the mechanisms for this remain unclear. Here we report that this genetic distance correlates with natural variation and epigenetic regulation of circadian clock-mediated stress responses. In intraspecific hybrids of Arabidopsis thaliana, genome-wide expression of many biotic and abiotic stress-responsive genes is diurnally repressed and this correlates with biomass heterosis and biomass quantitative trait loci. Expression differences of selected stress-responsive genes among diverse ecotypes are predictive of heterosis in their hybrids. Stress-responsive genes are repressed in the hybrids under normal conditions but are induced to mid-parent or higher levels under stress at certain times of the day, potentially balancing the tradeoff between stress responses and growth. Consistent with this hypothesis, repression of two candidate stress-responsive genes increases growth vigour. Our findings may therefore provide new criteria for effectively selecting parents to produce high-or low-yield hybrids.
Bibliographical noteFunding Information:
We thank Dr Enamul Huq and Dr Sibum Sung for their input to improve the manuscript, Dr Detlef Weigel for providing the acd6-1 mutant seeds and Dr Xing-Wang Deng for sharing the methylation data. This work was supported by grants (ISO1238048 and ISO1025947) from the National Science Foundation (Z.J.C.).