Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication
Abstract
Background: Understanding the evolutionary genetics of modern crop phenotypes has
a dual relevance to evolutionary biology and crop improvement. Modern upland cotton
(Gossypium hirsutum L.) was developed following thousands of years of artificial selection
from a wild form, G. hirsutum var. yucatanense, which bears a shorter, sparser, layer
of single-celled, ovular trichomes ('fibre'). In order to gain an insight into the
nature of the developmental genetic transformations that accompanied domestication
and crop improvement, we studied the transcriptomes of cotton fibres from wild and
domesticated accessions over a developmental time course. Results: Fibre cells were
harvested between 2 and 25 days post-anthesis and encompassed the primary and secondary
wall synthesis stages. Using amplified messenger RNA and a custom microarray platform
designed to interrogate expression for 40,430 genes, we determined global patterns
of expression during fibre development. The fibre transcriptome of domesticated cotton
is far more dynamic than that of wild cotton, with over twice as many genes being
differentially expressed during development (12,626 versus 5273). Remarkably, a total
of 9465 genes were diagnosed as differentially expressed between wild and domesticated
fibres when summed across five key developmental time points. Human selection during
the initial domestication and subsequent crop improvement has resulted in a biased
upregulation of components of the transcriptional network that are important for agronomically
advanced fibre, especially in the early stages of development. About 15% of the differentially
expressed genes in wild versus domesticated cotton fibre have no homology to the genes
in databases. Conclusions: We show that artificial selection during crop domestication
can radically alter the transcriptional developmental network of even a single-celled
structure, affecting nearly a quarter of the genes in the genome. Gene expression
during fibre development within accessions and expression alteration arising from
evolutionary change appears to be 'modular' - complex genic networks have been simultaneously
and similarly transformed, in a coordinated fashion, as a consequence of human-mediated
selection. These results highlight the complex alteration of the global gene expression
machinery that resulted from human selection for a longer, stronger and finer fibre,
as well as other aspects of fibre physiology that were not consciously selected. We
illustrate how the data can be mined for genes that were unwittingly targeted by aboriginal
and/or modern domesticators during crop improvement and/or which potentially control
the improved qualities of domesticated cotton fibre. See Commentary: http://www.biomedcentral.com/1741-7007/8/137
Type
Other articleSubject
oxidative stresssucrose synthase
cell-wall
arabidopsis-thaliana
maize domestication
functional genomics
iron homeostasis
plant-growth
evolution
cellulose
biology
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https://hdl.handle.net/10161/4375Published Version (Please cite this version)
10.1186/1741-7007-8-139Citation
Rapp,Ryan A.;Haigler,Candace H.;Flagel,Lex;Hovav,Ran H.;Udall,Joshua A.;Wendel,Jonathan
F.. 2010. Gene expression in developing fibres of Upland cotton (Gossypium hirsutum
L.) was massively altered by domestication. Bmc Biology 8( ): 139-139.
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