Cross-Species Bacterial Artificial Chromosome–Fluorescence in Situ Hybridization Painting of the Tomato and Potato Chromosome 6 Reveals Undescribed Chromosomal Rearrangements

Abstract

Ongoing genomics projects of tomato (Solanum lycopersicum) and potato (S. tuberosum) are providing unique tools for comparative mapping studies in Solanaceae. At the chromosomal level, bacterial artificial chromosomes (BACs) can be positioned on pachytene complements by fluorescence in situ hybridization (FISH) on homeologous chromosomes of related species. Here we present results of such a cross-species multicolor cytogenetic mapping of tomato BACs on potato chromosomes 6 and vice versa. The experiments were performed under low hybridization stringency, while blocking with Cot-100 was essential in suppressing excessive hybridization of repeat signals in both within-species FISH and cross-species FISH of tomato BACs. In the short arm we detected a large paracentric inversion that covers the whole euchromatin part with breakpoints close to the telomeric heterochromatin and at the border of the short arm pericentromere. The long arm BACs revealed no deviation in the colinearity between tomato and potato. Further comparison between tomato cultivars Cherry VFNT and Heinz 1706 revealed colinearity of the tested tomato BACs, whereas one of the six potato clones (RH98-856-18) showed minor putative rearrangements within the inversion. Our results present cross-species multicolor BAC-FISH as a unique tool for comparative genetic studies across Solanum species.

Chromatin Structure and Physical Mapping of Chromosome 6 of Potato and Comparative Analyses With Tomato

“…These results suggest that a potato/tomato inversion likely spans the entire euchromatic portion of the short arms of the chromosome 6. A similar pachytene chromosomebased FISH mapping using tomato BACs revealed the same potato/tomato inversion (Tang et al 2008).…”

“…In addition, an inter- stitial heterochromatic knob was consistently detected on the long arms of both USW1 and RH (Figure 1, a-c). This knob, however, was not observed in potato lines described by Tang et al (2008), which shows intraspecific variation of the heterochromatin distribution in the potato genome.…”

“…Meiotic pachytene chromosomes are superior to somatic metaphase chromosomes for FISH mapping 1 resolution (Cheng et al 2002). Integration of genetic linkage maps with pachytene chromosome-based cytogenetic maps has been reported in several plant species (Cheng et al 2001;Islam-Faridi et al 2002;Howell et al 2005;Kim et al 2005;Kulikova et al 2001;Walling et al 2006;Wang et al 2006;Amarillo and Bass 2007;Chang et al 2007;Koo et al 2008;Szinay et al 2008;Tang et al 2008, accompanying article, this issue). We report FISH mapping of 30 genetic marker-anchored BACs on the pachytene chromosome 6 of potato.…”

Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the World’s Third Most Important Food Crop

“…Recently, a method for using multi-colour FISH for BAC localization on the pachytene phase of meiosis chromosomes using directly labeled BAC probes has been developed (Tang et al 2008). Hybridization of repetitive DNA sequences from the BACs was effectively suppressed by adding an excess of unlabeled Cot100 genomic DNA to the hybridization mixture.…”

“…To this end, we have developed a cross-species multi-colour FISH strategy to reveal BAC positions in species related to potato and tomato (Tang et al 2008). …”