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.

Figure 1.—

(a) Chromosomes 6 of tomato and potato at the pachytene stage. S, short arm; L, long arm; Eu, euchromatin; Pc, pericentromere heterochromatin; Cen, centromere. (b) FISH of the tomato BACs H153O03 (red) and H073H07 (green) on tomato pachytene chromosome 6. (c) Cross-species FISH of the same BACs on potato chromosome 6. (d) FISH of H112G05 (red) and H24L21 (green) on tomato chromosome 6. (e) Cross-species FISH of the same BACs on potato chromosome 6. (f) Cross-species FISH of the tomato BACs H003K02 (green) and H309K01 (red) on potato chromosomes without Cot-100 blocking. (g and h) FISH of the potato BACs 67P23 (red) and 112M11 (green) on potato RH98-856-18 chromosome 6 (g) and tomato chromosome 6 (h). (i) The straightened part of chromosome 6 of potato (P) and tomato (T), showing the orientation and relative distance of the two potato BACs 67P23 (red) and 112M11 (green).

Figure 2.—

Examples of FISH and cross-species FISH of tomato BACs on pachytene chromosome 6 of tomato (T) and potato (P). The chromosome regions of interest were straightened and oriented with the signals close to the short arm telomere upward. (a) FISH of H107A05 (orange), H112G05 (green), and H304P16 (blue) on the short arms of tomato and potato showed a clear inverted arrangement of the BAC signals. (b) FISH of H153O03 (orange), H250I21 (red), and H112G05 (blue) showed an inverted order between the homeologs. (c) FISH of H054K13 (orange), H251G05 (green), H288L16 (red), and H304P16 (blue) showed an inverted order between the homeologs. Notably, here we used potato clone RH98-856-18, and the H251G05 (green) BAC produced a large and a small focus on the potato chromosome, suggesting a breakpoint in this BAC for a putative chromosomal rearrangement. (d) FISH of RH034P18 (green), 67P23 (red), RH026H24 (orange), 112M11 (pink), and RH69B12 (blue) showed an inverted order between the homeologs; RH069B12 did not give a signal on tomato. (e) FISH of H107A05 (orange), H250I21 (red), H097D13 (blue), and H059K09 (green) on the short arm. The two pericentromere heterochromatin BACs H097D13 (blue) and H059K09 (green) showed weak and variable foci on the potato short arm. (f) FISH of H309K01 (green), H003K02 (red), H194N16 (blue), and H309D09 (orange) on the long arm showed the same order of the BACs except H309K01 (green) hybridization that gave no signal in potato. (g) FISH of H026E06 (blue), H106K23 (green), H309D09 (orange), and H060A01 (red) on the long arm showed the same order on the tomato and potato chromosomes.

Figure 3.—

A comparison of genetic and physical maps for tomato BACs and cross-species FISH of tomato and potato BACs on pachytene chromosomes. The schematic drawings of the chromosomes are based on pachytene morphology. Black and dark gray blocks are heterochromatin regions; the dark blocks represent the dense brightly fluorescing heterochromatin regions, whereas the lighter regions are lighter and more variable; the white blocks are the centromeres. The BACs are positioned in sequence of FISH position. Brackets on the left of the BACs have the same genetic map positions; brackets on the right have overlapping FISH signals on the chromosome. The dotted lines show the position of their markers on the genetic map. BACs in bold italics are the potato BACs. The red bar between the tomato and potato chromosomes represents the short arm paracentric inversion; the green block indicates the positions of minor chromosome rearrangements between potato clone RH98-856-18 and the other five remaining potato lines. The question marks point at weak, variable, or no signals of the tomato BACs on potato.