The goal of the research in the Chen laboratory is to elucidate molecular and evolutionary mechanisms for advantages and disadvantages of polyploidy and heterosis and their impact on crop domestication and production. The understanding of these phenomena is among the grand challenges in plant biology and is vital to agriculture, food production, renewable energy, the environment, and human health. Most crop plants including wheat and cotton are polyploids, and many others such as maize are ancient polyploids and/or are grown as hybrids. Using genomic and molecular biology approaches, we investigate how and why the genomic mixture and epigenetic regulation alters circadian rhythms and regulatory networks to promote growth vigor in Arabidopsis hybrids and allopolyploids and how the circadian clock regulates growth vigor in maize hybrids. Although heterosis is common in hybrids and allopolyploids that overcome postzygotic barriers, some hybrids and allopolyploids cannot produce offspring, a phenomenon known as hybrid incompatibility. We test a hypothesis that molecular interactions between genes and small RNAs that are functionally diverged in the respective hybridizing species cause hybrid incompatibilities in Arabidopsis interspecific hybrids and allopolyploids. Finally, our research is extended from Arabidopsis polyploids to cotton allotetraploids. In addition to polyploidy, cottonseed hair development shares many similarities with Arabidopsis trichome development. Cotton fiber is an excellent model for the study of cellulose and cell fate determination. We are working towards sequencing of allotetraploid cotton genomes and a better understanding of fiber cell development for cotton improvement.