Homeologous recombination in Solanum lycopersicoides introgression lines of cultivated tomato

Abstract

A library of "introgression lines" containing Solanum lycopersicoides chromosome segments in the genetic background of cultivated tomato (Lycopersicon esculentum) was used to study factors affecting homeologous recombination. Recombination rates were estimated in progeny of 43 heterozygous introgressions and whole-chromosome substitution lines, together representing 11 of the 12 tomato chromosomes. Recombination within homeologous segments was reduced to as little as 0-10% of expected frequencies. Relative recombination rates were positively correlated with the length of introgressed segments on the tomato map. The highest recombination (up to 40-50% of normal) was observed in long introgressions or substitution lines. Double-introgression lines containing two homeologous segments on opposite chromosome arms were synthesized to increase their combined length. Recombination was higher in the double than in the single segment lines, despite a preference for crossovers in the region of homology between segments. A greater increase in homeologous recombination was obtained by crossing the S. lycopersicoides introgression lines to L. pennellii--a phylogenetically intermediate species--or to L. esculentum lines containing single L. pennellii segments on the same chromosome. Recombination rates were highest in regions of overlap between S. lycopersicoides and L. pennellii segments. The potential application of these results to breeding with introgression lines is discussed.

Figure 1.—

Genetic map of S. lycopersicoides introgression lines. The introgressed segments in each line are indicated by solid bars to the right of the chromosome maps. Thicker lines indicate regions homozygous for S. lycopersicoides markers. Numbers above the line are the accession identifiers (all “LA” numbers unless otherwise indicated). Dashed lines connecting marker loci to the introgressed segments indicate which markers were evaluated in each line. The locations of recombination events detected in progeny are indicated by 's. (An absence of 's in a given interval indicates no crossovers were detected). Recombination data are summarized in Table 1. The distances between markers are from Tanksley et al. (1992), and the positions of centromeres (0) are from Pillen et al. (1996). The location of a paracentric inversion on chromosome 10 that distinguishes cultivated tomato from S. lycopersicoides is shown by a dashed line with double arrowheads (from Pertuze et al. 2002).

Figure 2.—

Correlation between observed frequencies of homeologous recombination in S. lycopersicoides introgression lines (expressed as a percentage of the expected value) and the genetic length of introgressed segments on the tomato map. Observed recombination rates represent the combined map units of all marker intervals in each segment. The expected genetic lengths are the distances between corresponding markers on the RFLP map of tomato (Tanksley et al. 1992). Included in the correlation are four data points (open circles) representing recombination frequencies in substitution lines containing S. lycopersicoides chromosome 7 or 8 (SL-7, SL-8). Note that data on LA4276 are not included because this line carries an inverted segment that does not recombine.

Figure 3.—

Diagram illustrating the construction of double S. lycopersicoides introgression lines, and their possible use for increasing recombination frequency in the progeny. The “target” introgression line contains a homeologous segment with a gene of interest, such as a hypothetical disease resistance factor (R). (A) The “driver” line contains a homeologous segment on the opposite arm of the same chromosome. (B) The “bridging” introgression is a line containing a donor segment from L. pennellii. Each double-introgression line is heterozygous for two alien segments, initially in repulsion linkage phase, on the same chromosome. The locations of crossover events, predicted to occur preferentially in homologous stretches, are indicated with an . Representative recombinant chromosomes that are obtainable in the progeny are shown.

Figure 4.—

Recombination in “target/driver” double-introgression lines for chromosomes 1 (A), 2 (B), and 7 (C). For each chromosome, the location of the two introgressed segments is shown to the right of the reference map, based on recombination in F₂ L. esculentum × L. pennellii (F₂ esc × pen). The total map units in each interval are shown to the left of the reference map. Recombination in single introgressed segments served as controls for the corresponding double-introgression lines. Linkage estimates were obtained both from F₂ and from backcross (BC) progeny. The rate of recombination was measured both within the introgressed segments (solid regions, indicating homeology) and in the interval between them (open segments, indicating homology). The total number of individuals genotyped in each progeny array is indicated by n. The asterisk on the IL-7C map is to indicate that the control data for this marker interval were from a line with a slightly longer segment, extending beyond TG199 to marker TG216 (not shown on the map).

Figure 4.—

Recombination in “target/driver” double-introgression lines for chromosomes 1 (A), 2 (B), and 7 (C). For each chromosome, the location of the two introgressed segments is shown to the right of the reference map, based on recombination in F₂ L. esculentum × L. pennellii (F₂ esc × pen). The total map units in each interval are shown to the left of the reference map. Recombination in single introgressed segments served as controls for the corresponding double-introgression lines. Linkage estimates were obtained both from F₂ and from backcross (BC) progeny. The rate of recombination was measured both within the introgressed segments (solid regions, indicating homeology) and in the interval between them (open segments, indicating homology). The total number of individuals genotyped in each progeny array is indicated by n. The asterisk on the IL-7C map is to indicate that the control data for this marker interval were from a line with a slightly longer segment, extending beyond TG199 to marker TG216 (not shown on the map).

Figure 4.—

Recombination in “target/driver” double-introgression lines for chromosomes 1 (A), 2 (B), and 7 (C). For each chromosome, the location of the two introgressed segments is shown to the right of the reference map, based on recombination in F₂ L. esculentum × L. pennellii (F₂ esc × pen). The total map units in each interval are shown to the left of the reference map. Recombination in single introgressed segments served as controls for the corresponding double-introgression lines. Linkage estimates were obtained both from F₂ and from backcross (BC) progeny. The rate of recombination was measured both within the introgressed segments (solid regions, indicating homeology) and in the interval between them (open segments, indicating homology). The total number of individuals genotyped in each progeny array is indicated by n. The asterisk on the IL-7C map is to indicate that the control data for this marker interval were from a line with a slightly longer segment, extending beyond TG199 to marker TG216 (not shown on the map).

Figure 5.—

Genetic maps of recombination frequencies within S. lycopersicoides introgression lines for chromosome 2 in different genetic backgrounds. (A) Recombination in F₂ progeny of introgression line LS38-11 crossed to L. pennellii. (B) Genetic distances between the same markers taken from the RFLP map of tomato (Tanksley et al. 1992). (C) Recombination in F₂ progeny of LA4239 in the background of L. esculentum (data from Table 1). Chromosomes are shaded to indicate that the genetic distances are in centimorgans, based on the Kosambi mapping function. Map A consisted of two linkage groups at the threshold of LOD ≥ 3.0.

Figure 6.—

Recombination in “bridging” introgression lines containing introgressed segments from S. lycopersicoides and L. pennellii on chromosome 7. Dotted lines indicate the marker loci used to measure recombination within each segment and their positions on the RFLP map (Tanksley et al. 1992). Recombination frequencies are expressed as the percentage of the expected values for the same marker intervals. An indicates the region to which each recombination value applies. The positions of the L. pennellii segments are from Liu and Zamir (1999). The controls are the lines containing a single introgressed segment, either from S. lycopersicoides (LA4259) or from L. pennellii. The single-segment L. pennellii controls were genotyped with the same markers as the corresponding segments in the double-introgression stocks. Recombination estimates are based on F₂ populations (of size n) corresponding to the crosses indicated above the chromosomes. Single-introgression lines were crossed to L. esculentum cv. M82 or VF36 so that all recombination tests were carried out in a constant genetic background, equivalent to F₁ VF36 × M82.