UC Davis

Structural variation plays an important role in plant genome architecture and phenotypes. It is also suggested to be a new type of DNA marker for genomic selection in plant breeding. While many studies have characterized the properties and effects of structural variation on crops, its origin and the interplay with other genetic factors still remain unclear. This study investigated the origin of complex genomic structural variation, as well as the interplay between induced structural variation and natural nucleotide polymorphism on plant phenotypes. One novel type of structural variation characterized recently is chromoanagenesis. Chromoanagenesis is described as a catastrophic event resulting in chromosomal restructuring on a localized region, mostly involving one single chromosome. Although chromoanagenesis has been largely characterized in animal cells, its presence and origin in plants have not been determined. Sequencing of the genomes of a gamma irradiation-mediated Populus hybrid population detected 2 F1 lines carrying shattered chromosomes. One line exhibited shattered patterns on chromosome 1 and the other on chromosome 2. Novel DNA junctions were identified and validated in these 2 lines, and the results confirmed that the reorganized segments were consistent with what is expected as the product of chromoanagenesis. Genomic features enrichment analysis indicated that breakpoints were likely to occur in gene rich regions. Chromoanagenesis-like patterns were also observed in a hybrid Arabidopsis thaliana line carrying the asy1 mutation. Short-read sequencing revealed that the shattered pattern was on chromosome 1. 249 novel DNA junctions were identified with both ends associated with shattered regions. As in the Populus case, breakpoints were significantly enriched in genic regions. SNP frequency analysis revealed that the restructured chromosome resulted from mis-segregation at Meiosis I in the maternal parent. These two cases suggested that chromoanagenesis can originate from mutagenesis in plants. To further characterize structural variation and document their effect on plant phenotypes, we decided to investigate the effects of structural variation in forest trees, whose structural variation studies are relatively new. Highly polymorphic forest trees are expected to carry high levels of allelic and dosage variation, and the interaction of these two types of variation and their combined effect on phenotype is unclear. In a Populus hybrid population, QTL analysis was performed to document the effect of two types of variation on traits - natural allelic variation and induced dosage variation. Results suggested that QTLs from allelic and dosage variation were independent. Integrating the QTLs from both allelic and dosage variation exhibited significant improvement on phenotypic variance explanation compared to only allelic or dosage QTLs. These findings provide a snapshot of the relationship between allelic and structural variation and their effects on plant phenotypes.