Research related to crop domestication has been transformed by technologies and discoveries …

• Abstract
• Introduction
• Fine-resolution mapping and gene cloning of domestication-related genes
• Domestication trait alleles can be found in wild populations
• Orthologues of domestication genes and their action
• Effects of selection on domestication genes
• Gene evolution
• Gene and genome duplication
• Achieving new levels of crop yield and new uses for crops
• Super domestication
• Literature cited
• Figure

There are many different families of transcriptional regulatorsin plants and the transcriptional regulators involved in domesticationdiscussed by Doebley et al. (2006) all belong to different families.Within a given family of transcriptional regulators, gene structuremay be sufficiently conserved for similarities to be identifiednot just between genera of the same plant family but betweentaxonomically very distantly related species. Thus, monoculm1in maize shares similarities with LATERAL SUPPRESSOR from Arabidopsisthaliana and tomato (see Doust, 2007, in this Special Issue)and Q in wheat is similar to APETALA2 (AP2) of Arabidopsis (Simons et al., 2006).AP2-like genes appear to have a wide range of roles in plantdevelopment, but Q is so far the only AP2-like gene implicatedin domestication (Simons et al., 2006). One of the genes affectingshattering in rice, qSH1, may be an orthologue of REPLUMLESS(RPL) in Arabidopsis (Konishi et al., 2006). REPLUMLESS is involvedin formation of an abscission layer in the wall of the fruit,whereas qSH1 affects formation of an abscission layer betweenpedicel and spikelet, but Konishi et al. (2006) suggest thatthis difference could be explained by differences in the transcriptionalcontrol of RPL and qSH1. The duplicate genes zfl1 and zfl2 ofmaize are orthologous to the FLORICAULA/LEAFY (FLO/LFY) genesof species of Antirrhinum and Arabidopsis, amongst others (Bomblies and Doebley, 2006).Among the various effects suggested for these genes is the changein phyllotaxy that produces whorled organs during flower development.In maize, zfl2 is the candidate gene for a major effect QTLcontrolling the whorled versus two-ranked arrangement of femalespikelets in maize versus teosinte. FLO/LFY-like genes havenot been reported to affect inflorescence phyllotaxy in anyother species, but Bomblies and Doebley (2006) suggest thata change in expression pattern could have allowed one of theirorthologues to be annexed for a new role in maize.

Rice contains an orthologue of maize tb1, OsTB1, that, likemaize tb1, affects lateral branching (Takeda et al., 2003).Transgenic rice carrying an extra dose of OsTB1 produced manyfewer tillers than normal because of over-expression of OsTB1.A known mutant, fine culm1 (fc1), with enhanced tiller production,mapped to the same locus as OsTB1, suggesting that fc1 is anallele of OsTB1. Sequencing of fc1 showed a deletion generatinga premature stop codon, such that the predicted polypeptideproduct lacked the domain implicated in the DNA binding activityof the class of transcriptional regulators to which tb1 belongs.Takeda et al. (2003) therefore suggest that alterations in theexpression of OsTB1 through dosage effects or use of mutantscould be used to increase or decrease tiller number at willand thereby adapt rice morphology to differing agronomic situations(see also Doust, 2007, in this Special Issue).

In the major oilseed crop canola or oilseed rape (Brassica juncea,B. napus and B. rapa) losses of between 10–50 % of yieldcan occur due to unsynchronized pod shattering (Østergaard et al., 2006)and require extensive management, including spraying with cropdessicants before harvest and windrowing before threshing. Arabidopsishas proved to be a useful model to study the phenomenon, wherea transcriptional regulator, FRUITFUL (FUL), mediates pod dehiscenceby inhibiting expression of genes controlling shattering. Whenthis transcriptional regulator was introduced in B. juncea itwas over-expressed and pods had no shattering. Further fine-tuningof the expression of this gene in canola may enable the requiredlevel of post-harvest shattering to be achieved (Østergaard et al., 2006).Such intentional manipulations to fine-tune gene activity willcertainly constitute super-domestication, where genetics interactswith crop management and agronomy.

Evidently much remains to be learned about the actions of transcriptionalregulators and how they in turn are regulated. Recently, Clark et al. (2006)located a factor or factors controlling the levels of the messageproduced by the transcriptional regulator teosinte branched1 (tb1) in maize, and hence the phenotypic differences betweenmaize and teosinte associated with tb1, to an intergenic regionupstream from tb1. This region consists of a mixture of repetitiveand unique sequences not previously considered to contributeto phenotypic variation. Doebley and Lukens (1998) had earlierproposed that modifications in cis-regulatory regions of transcriptionalregulators would prove a predominant means for the evolutionof novel forms, and the findings of Clark et al. (2006) appearto provide a supporting example. Plant-breeding-related companiesare already looking at the effects of up- and downregulatingall transcription factors in a given genome, aiming to learnmore about the target genes of different transcription factorsand producing a super-domesticate (Doebley et al., 2006), perhapswith more success than gene mutation as a source of Dobzhansky's‘hopeful monsters’.