Polyploidy has played a spectacular role in plant evolution. Through allopolyploidization, two or more divergent genomes are combined into a common nucleus, which is often followed by rapid as well as longer-term genomic and epigenetic responses. However, since mRNA abundance and protein amounts are poorly related, still little is known how the genomic changes associate with or affect the actual plant function and adaption. Within this context, this dissertation specifically explores the evolutionary history of cotton species on the proteomic level, involving natural polyploidization and human-mediated cotton fiber selection.
In the work presented here, cotton proteomes of mature seeds and developing fibers were examined to understand the genome-wide proteomic changes accompanying allopolyploidization. Interspecific comparisons of protein composition and expression level among diploid and polyploid cotton species revealed that the allopolyploid cotton display asymmetric proteomic divergence with respect to the diploid progenitors, which is detailed by describing important phenomena of non-additive expression, expression level dominance and homoeolog expression bias.
To understand the genome-wide expression changes associated with domestication, the fiber proteomes represented by four representative developmental stages were studied for two important crop species - G. hirsutum and G. barbadense, using paired wild and domesticated accessions. By contrasting the fiber proteomes and developmental dynamics between wild and domesticated accessions for each species, we were able to characterize the key features of global protein pattern change corresponding to the domestication processes. Furthermore, we identified a number of proteins differentially expressed during fiber development and altered by domestication, as candidate proteins and metabolic processes for functional analyses that may yield insight into domestication and future cotton improvement
