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Gene and genome duplication
- From Crop Domestication to Super-domestication

An area where DNA technologies have had a particular impacton our understanding of domestication has been in relation togene and genome duplication. As well as polyploidy, gene duplicationis a common evolutionary phenomenon in plants (for review seeMoore and Purugganan, 2005). In maize it has been estimatedthat about a third of genes are tandem duplicates due to unequalrecombination or transposition events that have involved genefragments (Emrich et al., 2007). Rondeau et al. (2005) haveshown duplication and subsequent functional specialization ofNADH-MDH genes in some, but not all, grasses with C4 photosynthesis.Among duplicated genes are a class called nearly identical paralogs(NIPs) that appear to be of recent origin. This class of duplicategene shares ≥98 % identity. Many NIPs in maize are differentiallyexpressed. This has lead to the suggestion that the variationin this class of duplicate gene provides new variation thatmay have had a selective advantage during domestication andimprovement of maize (Emrich et al., 2007), and again modellingof plant architecture may suggest routes for crop improvement(Guo et al., 2006).

Reflecting the abundance of polyploids in the plant kingdom,many important crops exhibit both allopolyploidy (e.g. wheat,canola, tobacco, peanut and cotton) and autopolyploidy (e.g.watermelon, strawberries, potato and alfalfa). Allopolyploidyresults in increased allelic diversity while autopolyploidyresults in increased allelic copy number, both of which canlead to novel phenotypes. Since polyploidy is so common in plantsthey must have some selective advantages. Among the presumedmain advantages of polyploidy are fixation of heterosis, duplicationenabling evolution of gene function, and alteration of regulation.

The allopolyploid oilseed crop Brassica napus (canola) providesan example of how heterozygosity resulting from polyploidy canaffect evolutionarily important traits. Brassica napus is thoughtto be derived from crosses between B. oleracea (2n = 18, CCgenome) and B. rapa (2n = 20, AA genome). Using molecular markers,lines in mapping populations were compared at a transpositionsite with QTL for seed yield (Osborn et al. 2003a, Quijada et al., 2006,Udall et al., 2006). When the allelic arrangement was similarto that of the parental genotypes, B. oleracea and B. rapa,seed yields were lower. However, when the arrangement of allelesdiffered from these parental genotypes seed yields were higher.The best explanation for the results of these studies was thatintergenomic heterozygosity increased seed yield in B. napus.

In allopolyploid cotton, an ancient polyploidy, it has beenshown that some homoeologous genes are assigned to different(sub)functions, with gene expression compartmentalized to differenttissue types and gene expression biased between homoeologs (Adams et al., 2003,2004). Thus, between the genomes of cotton, expression of homoeologousgenes is developmentally regulated. It has been suggested thatthis may provide allopolyploids with greater plasticity in responseto stress (Udall and Wendel, 2006). Further understanding ofwhat causes changes in homoeologous gene function may provideavenues to manipulate gene expression.

Gene expression is generally dependent on hierarchically organizednetworks of regulators. The number of these regulators can beincreased several-fold in polyploids and the overall consequencesof polyploidy on gene expression at the end of regulatory networksare difficult to predict (Osborn et al., 2003b). In a genome-wideanalysis of synthetic allotetraploids between Arabidopsis thalianaand A. arenosa, about 5 % of genes showed divergence from themid-parent value, suggesting non-additive gene regulation (Wang et al., 2006b).For example, time of flowering in this synthetic allopolyploidwas later than both parents. This was found to be the resultof the epistatic interactions between two loci, one for floweringfrom A. thaliana (FLC) and the other from A. arenosa (FRI),that enhances FLC expression and inhibits flowering (Wang etal., 2006a). In hexaploid wheat, latitude of breeding has influencedthe selection of genes affecting earliness of flowering, butthere is still much genetic diversity relating to both photoperiodand vernalization requirements of the selections (Goldringer et al., 2006).The rapid reprogramming of biological pathways on polyploidizationleads to novel variation that may be exploited by plant breeders.

Many breeding programmes involve wide and distant hybridization.These procedures cause dramatic genome change, sometimes leadingto unpredictable results. Studies of ancient and modern polyploidsprovide a means of elucidating the effects of dramatic genomechange on gene expression and regulation. Results from suchstudies should enable breeding programs to achieve the desiredresults.

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