Molecular techniques are not just enabling the position of domestication-relatedgenes to be resolved but they can provide information on theeffects of selection and number of generations required fordomestication. By studying nucleotide polymorphism in differentaccessions of a crop upstream and downstream from domestication-relatedgenes, it is possible to determine the extent to which selectionis acting across the genome, the selective sweep (Clark et al., 2004).Positive directional selection leads to reduced variation andlinkage disequilibria in the respective regions (Palaisa et al., 2004).By comparing sequence diversity around a domestication genein the crop and its progenitor, a new view of the processesthat sculptured the formation of the crops species can be attained.By analysis of nucleotide polymorphism around the teosinte branched1 (tb1) gene in a wide variety of maize accessions, it was foundthat human selection acted on the gene's regulatory region andwas not detected in the protein-coding region (Wang et al., 1999;Clark et al., 2004). This was considered to be a consequenceof the high rates of recombination in maize. From the analysisit was estimated that the time taken to domesticate maize wasbetween 315–1023 years (Wang et al., 1999). Studies ofwheat remains at archaeological sites in southern Turkey andSyria, where wheat domestication is believed to have occurred,reveal a gradual change from dehiscent to indehiscent spikelets,suggesting indehiscence took over one millennium to become established(Tanno and Wilcox, 2006). Archaeological remains of rice fromthe lower Yangtze river suggests that rice domestication wasa slow process (see Fuller, 2007, in this Special Issue) andthis is supported by the wild-rice harvesting methods used today,which do not provide a selection pressure for non-shatteringspikelets (Fig. 1). Both molecular and archaeobotanicalstudies suggest a long period of gathering and cultivation precededdomestication for these cereals. While domestication representsrapid change in evolutionary terms, in cereals the transitionin the suite of characters that changed wild populations intodomesticated crops took place over many centuries or millennia.
During domestication, population genetic diversity is reducedas a consequence of selection. Domestication-related genes experiencea more severe genetic bottleneck due to selection than neutralgenes, as discussed by Doebley et al., (2006) and in this SpecialIssue by Yamasaki et al. (2007). Estimates of the severity ofthe genetic bottleneck of domestication based on comparisonof genetic diversity found in their wild ancestors vary considerablyfrom about 80 % in maize (Wright and Gaut, 2005), to 40–50% in sunflower (Liu and Burke, 2006) and as little as 10–20% in rice (Zhu et al., 2007). Polyploid wheats have sufferedtwo bottlenecks associated with the transition from wild wheatand also due to polyploidy. Thus, hexaploid bread wheat hasabout 7 % and 30 % of the nucleotide diversity of its D andA/B genome donors, respectively (Dubcovsky and Dvorak, 2007).Determining how much diversity is lost during the genetic bottleneckof domestication can suggest approaches to future crop improvement,such as tapping high diversity gene sources in wild progenitors(Whitt et al., 2002) or transgenic alteration of expressionof selected genes (see Yamasaki et al., 2007, in this SpecialIssue).
Detection of previously undetected domestication-related geneshas become possible using QTL analysis and selective sweepsacross the genome (Yamasaki et al., 2007). This enables hiddendomestication genes to be detected based on the selection profileof comparative sequences. Genomic comparison of crops and theirwild progenitors for hidden domestication-related genomic regionsis a new approach to detecting potentially useful diversityin wild progenitors for crop improvement.