Abstract
SummaryPolyploidy, the possession of multiple sets of chromosomes, has been a predominant factor in the evolution and success of the angiosperms. Although artificially formed allopolyploids show a high rate of genome rearrangement, the genomes of cultivars and germplasm used for crop breeding were assumed stable and genome structural variation under the artificial selection process of commercial breeding has remained little studied. Here, we show, using a repurposed visualization method based on transcriptome sequence data, that genome structural rearrangement occurs frequently in varieties of three polyploid crops (oilseed rape, mustard rape and bread wheat), meaning that the extent of genome structural variation present in commercial crops is much higher than expected. Exchanges were found to occur most frequently where homoeologous chromosome segments are collinear to telomeres and in material produced as doubled haploids. The new insights into genome structural evolution enable us to reinterpret the results of recent studies and implicate homoeologous exchanges, not deletions, as being responsible for variation controlling important seed quality traits in rapeseed. Having begun to identify the extent of genome structural variation in polyploid crops, we can envisage new strategies for the global challenge of broadening crop genetic diversity and accelerating adaptation, such as the molecular identification and selection of genome deletions or duplications encompassing genes with traitâcontrolling dosage effects.
Highlights
Polyploid organisms have multiple sets of chromosomes, and genome studies indicate that the evolutionary flexibility endowed by polyploidy has shaped the genomes of most if not all eukaryotes (Comai, 2005)
As copy number variation (CNV) are frequently associated with genetic traits (Beckmann et al, 2007), they are likely to be of crucial importance to crop science as many important crops are recently formed polyploids
Analysis of differential gene expression into the nine categories indicative of genome dosage changes as listed in Table 1 (Data S3, S4 and S5) revealed numerous clearly defined blocks in the genome where many nearby genes showed the same directionality of one genome over-expressed with the other genome under-expressed, suggestive of potential blocks of homoeologous exchange
Summary
Polyploid organisms have multiple sets of chromosomes, and genome studies indicate that the evolutionary flexibility endowed by polyploidy has shaped the genomes of most if not all eukaryotes (Comai, 2005). Stable polyploidy occurs in fish and frogs (Gregory and Mable, 2005), plants offer the best systems for its study as this is where it is most widespread. It has been considered a predominant factor in the evolution and success of the angiosperms (Leitch and Bennett, 1997; Wendel, 2000). As part of the genome stabilization process termed âdiploidizationâ (Hillier et al, 2004; Wang et al, 2005), newly formed polyploid genomes undergo rapid structural evolution, including gene copy number variation (CNV) (Adams and Wendel, 2005). The lack of cost-effective analysis tools means that there has been relatively little analysis of genome structural variation in commercial varieties of polyploid crops
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