Genome-wide structural and gene content variations are hypothesized to drive important phenotypic variation within a species. Structural and gene content variations were assessed among four soybean (Glycine max) genotypes using array hybridization and targeted resequencing. Many chromosomes exhibited relatively low rates of structural variation (SV) among genotypes. However, several regions exhibited both copy number and presence-absence variation, the most prominent found on chromosomes 3, 6, 7, 16, and 18. Interestingly, the regions most enriched for SV were specifically localized to gene-rich regions that harbor clustered multigene families. The most abundant classes of gene families associated with these regions were the nucleotide-binding and receptor-like protein classes, both of which are important for plant biotic defense. The colocalization of SV with plant defense response signal transduction pathways provides insight into the mechanisms of soybean resistance gene evolution and may inform the development of new approaches to resistance gene cloning.

Polyploidy is remarkably common in the plant kingdom and polyploidization is a major driving force for plant genome evolution. Polyploids may contain genomes from different parental species (allopolyploidy) or include multiple sets of the same genome (autopolyploidy). Genetic and epigenetic changes associated with allopolyploidization have been a major research subject in recent years. However, we know little about the genetic impact imposed by autopolyploidization. We developed a synthetic autopolyploid series in potato (Solanum phureja) that includes one monoploid (1x) clone, two diploid (2x) clones, and one tetraploid (4x) clone. Cell size and organ thickness were positively correlated with the ploidy level. However, the 2x plants were generally the most vigorous and the 1x plants exhibited less vigor compared to the 2x and 4x individuals. We analyzed the transcriptomic variation associated with this autopolyploid series using a potato cDNA microarray containing $9000 genes. Statistically significant expression changes were observed among the ploidies for $10% of the genes in both leaflet and root tip tissues. However, most changes were associated with the monoploid and were within the twofold level. Thus, alteration of ploidy caused subtle expression changes of a substantial percentage of genes in the potato genome. We demonstrated that there are few genes, if any, whose expression is linearly correlated with the ploidy and can be dramatically changed because of ploidy alteration. Polyploids originate from either sexual reproduction via 2n gametes or somatic chromosome doubling. By traditional definition, there are two forms of polyploidy: allopolyploidy and autopolyploidy. These terms are often used to imply the mode of polyploid formation, but more accurately describe the degree of similarity between the subgenomes in polyploids. Allopolyploids have distinct subgenomes and typically originate from interspecific hybridization between divergent progenitor species. Autopolyploids have (nearly) identical subgenomes and typically originate from intraspecific hybridization (or self-fertilization through 2n gametes) or somatic chromosome doubling. Allo-and autopolyploids have traditionally been distinguished by modes of chromosome pairing and inheritance, with allopolyploids exhibiting bivalent pairing and disomic inheritance and autopolyploids exhibiting multivalent pairing and polysomic inheritance.A number of well-known polyploid plants of agricultural interest are classical allopolyploids, which include important crops such as bread wheat (2n ¼ 6x ¼ 42) and cotton (2n ¼ 4x ¼ 56). Studies of genetic and epigenetic changes associated with polyploidization have been focused mostly on newly synthesized allopolyploid materials 1 Present address:

Potato (Solanum tuberosum) is the third most important food crop in the world. Potato tubers must be stored at cold temperatures to prevent sprouting, minimize disease losses, and supply consumers and the processing industry with highquality tubers throughout the year. Unfortunately, cold storage triggers an accumulation of reducing sugars in tubers. Hightemperature processing of these tubers results in dark-colored, bitter-tasting products. Such products also have elevated amounts of acrylamide, a neurotoxin and potential carcinogen. We demonstrate that silencing the potato vacuolar acid invertase gene VInv prevents reducing sugar accumulation in cold-stored tubers. Potato chips processed from VInv silencing lines showed a 15-fold acrylamide reduction and were light in color even when tubers were stored at 4°C. Comparable, low levels of VInv gene expression were observed in cold-stored tubers from wild potato germplasm stocks that are resistant to cold-induced sweetening. Thus, both processing quality and acrylamide problems in potato can be controlled effectively by suppression of the VInv gene through biotechnology or targeted breeding.