Comparative Oligo-FISH Mapping: An Efficient and Powerful Methodology To Reveal Karyotypic and Chromosomal Evolution

TLDR

Karyotype development depends on identifying individual chromosomes, a task that remains difficult for most nonmodel plant and animal species. The authors created a new chromosome identification system that labels specific oligonucleotides on every chromosome. They designed 54,672 45‑nt oligos from single‑copy potato sequences, producing 26 distinct FISH signals that act as a barcode to uniquely label each of the 12 chromosomes in diploid and polyploid potato species and validated chromosomal rearrangements with oligo‑based painting. The barcode worked across Solanum species, allowing accurate karyotyping of six species diverged >15 MY, revealing two reciprocal translocations, and proving the technique’s utility for nonmodel plant chromosome research.

Abstract

Abstract Development of a eukaryotic karyotype relies on identification of individual chromosomes in the species, which has been accomplished only in a limited... Developing the karyotype of a eukaryotic species relies on identification of individual chromosomes, which has been a major challenge for most nonmodel 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 “bar code” or “banding pattern” to uniquely label each of the 12 chromosomes from both diploid and polyploid (4× and 6×) potato species. Remarkably, the same bar code can be used to identify the 12 homeologous 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 >15 MY. These six species have maintained a similar karyotype; however, modifications to the FISH signal bar code led to the discovery of two reciprocal chromosomal translocations in Solanum 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 nonmodel plant species.