If there was an intervention we should see genetic changes to crops that vastly exceed the rate of change if these plants had be subjected to pressure via selective breeding alone. I would be interested to know if this is the case.
I found an example, it shows that the 5' UTR associated with tb1 faced far more selection pressure than the coding region of tb1; in other words, more selection pressure was applied to that region of the genome which does NOT express a phenotype than to its associated allele:
Selection on Candidate Genes and Linked RegionsTests for selection have been applied most commonly to data from genes for which there has been a priori evidence of a role in domestication or crop improvement. One example is tb1 in maize, where
the pattern of nucleotide polymorphism was particularly striking ( Wang et al., 1999). As expected after a domestication bottleneck, the coding region of tb1 contains less genetic diversity in maize than teosinte; the maize coding region retains ∼40% of the genetic diversity in teosinte.
The more surprising observation was that the reduction in diversity was far more severe in the 5′ untranslated region (UTR), where maize retains only 2% of teosinte diversity. Further, the pattern changed abruptly over a narrow ∼100 base pair region. Based on these observations, Wang et al. (1999) made two conclusions. First, they concluded that selection targeted the tb1 5′ UTR during domestication, consistent with previous observations that tb1 expression differs between maize and teosinte ( Doebley et al., 1997). Second,
based on the abrupt shift in the pattern of diversity, they concluded that recombination had been sufficient to uncouple the history of the 5′ UTR from the coding region.
...
Notably, the cultivated sh4 allele weakens, but does not fully eliminate, the shattering phenotype, which might be critical, because farmers need seed that stays on the plant long enough to be harvested but which can subsequently be freed from the plant by threshing.
Finally, the ability to detect selection also depends on the history of the favored allele. Selection can be difficult to detect if the beneficial variant pre-existed as a common neutral polymorphism prior to domestication (Innan and Kim, 2004 and Przeworski et al., 2005). In this special case, the variant had the opportunity to recombine onto a number of haplotypes prior to the onset of selection. When selection commenced, it favored the variant and dragged along multiple linked haplotypes. These different haplotypes may encompass substantial genetic diversity.
As a result, selection does not substantially reduce genetic diversity around the selected site, and nucleotide polymorphism data may not provide a clear signature of a selection event. However, it is not clear whether this model conforms to reality. Many mutations for domestication traits, such as shattering, would have been deleterious in the wild population; thus, it is unlikely that such variants pre-existed as common, neutral alleles in wild populations.http://www.sciencedirect.com/science/article/pii/S0092867406015923
