Several highly domesticated plants such as maize, rice and wheat express domestication traits and have lost their ability to survive on their own in the wild [ 5].
Many of the genes that are differentially expressed in domesticated and wild cotton are 'cotton-specific', as inferred from the lack of significant sequence similarity with other nucleic acid and protein sequences in the National Center for Biotechnology Information database.
Overall, 9,465 genes, or almost a quarter of all genes surveyed, were differentially expressed in the domesticated cotton compared to wild cotton.
However, the initiation of exogenous feeding did not increase the number of differentially expressed transcripts between domesticated fish and their hybrids, despite the expected fading of maternal effects in later life stages [ 59].
During early exogenous feeding, the digestive and endocrine systems as well as carbohydrate, energy and lipid metabolism pathways are more highly expressed in the domesticated strain, while environmental information processing and immune pathways, especially those related to cytokines, are suppressed compared to those of wild stock.
For all genes diagnosed as differentially expressed between wild and domesticated G. hirsutum, estimates of their expression intensities according to the SAS model described above were recovered using lsmeans.
Our results show that, at any given time point, more than 1500 genes, or about 3.8% of those assayed are differentially expressed between wild and domesticated G. hirsutum, showing the genomic scale of gene expression change accompanying an altered developmental allometry within a single cell (increased fibre length in domesticated TM-1).
DAVID identified seven functional categories that were overrepresented among all genes differentially expressed between wild and domesticated zebrafish.
Across the developmental stages studied, a total of 9465 unigenes were differentially expressed between wild and domesticated cotton fibre.
A total of 612 probe sets were initially identified as differentially expressed between wild and domesticated strains.
