Comparative oligo-FISH Mapping: An Efficient and Powerful Methodology to Reveal Karyotypic and Chromosomal Evolution

Developing the karyotype of a eukaryotic species relies on identification of individual chromosomes, which has been a major challenge for most non-model plant and animal species. We developed a novel chromosome identification system by selecting and labeling oligonucleotides (oligos) located in specific regions on every chromosome. We selected a set of 54,672 oligos (45 nt) based on single copy DNA sequences in the potato genome. These oligos generated 26 distinct FISH signals that can be used as a 9barcode9 or a 9banding pattern9 to uniquely label each of the 12 chromosomes from both diploid and polyploid (4x and 6x) potato species. Remarkably, the same barcode can be used to identify the 12 homoeologous chromosomes among distantly related Solanum species, including tomato and eggplant. Accurate karyotypes based on individually identified chromosomes were established in six Solanum species that have diverged for more than 15 million years. These six species have maintained a similar karyotype, however, modifications to the FISH signal barcode led to the discovery of two reciprocal chromosomal translocations in S. etuberosum and S. caripense . We also validated these translocations by oligo-based chromosome painting. We demonstrate that the oligo-based FISH techniques are powerful new tools for chromosome identification and karyotyping research especially for non-model plant species.