Understanding the processes by which genetic variation accumulates in clonally propagated plants is critical for exploring their adaptive potential and maintaining their lasting viability. This has been investigated in clonally propagated diploids, especially in the context of grapevine and tree crop bud sports of agronomic interest, but less so in polyploids, where genetic redundancy and buffering of gene dosage imbalance permit exploration of additional variation space. Somatic variation also has been documented after cultured cells are induced to regenerate whole plants; the resulting “somaclonal variation” is noticeable because of its severe and often undesirable phenotypic effects. To investigate genomic variation among polyploid clones, we compared whole-genome sequencing of five clones of the tetraploid potato cultivar Desiree and eight protoplast-regenerated derivatives of one Desiree clone. We document single-nucleotide and structural variation among clonally propagated isolates of Desiree. In protoplast-regenerated clones, we found chromosome structural variation consistent with homologous and non-homologous DNA repair with apparent preferences for certain chromosomal locations. These events are consistent with the existence of genome instability at fragile sites, which exhibited either chromoanagenesis or copy-neutral loss of heterozygosity. Our observations provide a framework for understanding genome instability and its consequences in clonally propagated polyploids, and may even suggest strategies for plant genome engineering.
Coauthors: Benny Ordoñez – UC Davis;Xin Zhao – UC Davis;Guilherme Braz – Michigan State University;Michelle Fossi – UC Davis;Isabelle Henry – UC Davis;Jiming Jiang – Michigan State University;Luca comai – UC Davis