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Fine-resolution mapping and gene cloning of domestication-related genes
- From Crop Domestication to Super-domestication

Plants have relatively few morphological traits that are controlledby single genes with distinct alleles showing Mendelian segregation– Mendel was fortunate to find seven independent and non-interactinggenes. The development of molecular markers to analyse directlyDNA or gene products has meant that tens of thousands of segregatingpolymorphisms can be analysed in a species. This has made itpossible to locate genes controlling both qualitative and quantitativecharacters very precisely within the genome, understand theirinteractions, and then to study the phenotypic effects of individualgenes or small regions of chromosome in segregating populations(Paterson, 2002; Hancock, 2005; Zhang et al., 2005). In a numberof studies, quantitative trait loci (QTL) affecting differentelements of the domestication syndrome are collocated to thesame locus or the same small chromosomal region, suggestingeither pleiotropy or close linkage of the gene(s) concerned.It can be difficult to distinguish pleiotropy from close linkage(Bomblies and Doebley, 2006) but in this Special Issue, Weeden (2007)gives some examples of pleiotropy in pea; other examples arediscussed below.

Fine mapping of genes has led to the ability to clone domestication-relatedgenes and unravel the molecular basis of domestication-relatedchanges. For example, the two genes that are most importantin relation to spikelet shattering in rice (sh4 and qSH1) havebeen cloned (Konishi et al., 2006; Li et al., 2006; discussedby Sweeney and McCouch, 2007, in this Special Issue). sh4 isthe key shattering gene that distinguishes cultivated from wildrice, while the qSH1 gene controls the difference in the degreeof shattering between some indica and japonica varieties ofrice. sh4 is a transcription regulator and a single amino acidsubstitution results in reduced shattering. For qSH1 a singlenucleotide in the regulatory region of this gene results inthe altered level of seed shattering. sh4 activates the abscissionprocess while qSH1 regulates abscission-layer formation. Sequenceanalysis of sh4 has revealed a single base-pair mutation thatis responsible for non-shattering and this change is the samein both indica and japonica rice varieties (Lin et al., 2007).This result raises doubts about whether Asian rice was domesticatedmore than once, as has been suggested in several recent papers(for a review see Sang and Ge, 2007). In contrast, sequencingand comparing seven loci in wild and landrace barley have providedstrong evidence that barley was domesticated once in the FertileCrescent and a second time between 1500 and 3000 km to the east(Morrell and Clegg, 2007). Analysis of domestication genes acrossdiverse germplasm can resolve questions about where, from whatand how many times a crop was domesticated.

Differences in nucleotide sequence and/or levels of transcriptionof different alleles of transcriptional regulators affect thephenotypes produced by target genes. In wheat, the Q gene ispleiotropic for many domestication traits. The wild-type alleleq is associated with a fragile rachis and grain that does notthresh free of the chaff, whereas the domestication allele Qis associated with a tough rachis and free-threshing grain (Simons et al., 2006).Comparison of the structure and activity of these two allelessuggests that q is transcribed at lower levels than Q and thatthe q protein functions less efficiently than the protein productof Q (Simons et al., 2006). Q is not known in the wild progenitorsof wheat, but human selection post-domestication seems to haveresulted in up-regulation of Q such that Q has more than twicethe effect of q (Simons et al., 2006). Similarly, some of thedifferences in branching and spikelet suppression distinguishingdomesticated maize from wild teosinte and controlled by tb1have been attributed to up-regulation of tb1 in maize (Hubbard et al., 2002).To date, most domestication genes that have been cloned arediverse transcription factors that are usually functional (Doebley et al., 2006;Komatsuda et al., 2007). Thus the role of human selection onwild populations during crop domestication at the gene levelhas been modification rather than elimination of gene function(Consonni et al., 2005; Doebley et al., 2006). This perhapsreflects the relative rarity of mutations leading to new structuralor functional genes and the short time span of crop domestication.

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