Sex-specific crossover distributions and variations in interference level along Arabidopsis thaliana chromosome 4

Abstract

In many species, sex-related differences in crossover (CO) rates have been described at chromosomal and regional levels. In this study, we determined the CO distribution along the entire Arabidopsis thaliana Chromosome 4 (18 Mb) in male and female meiosis, using high density genetic maps built on large backcross populations (44 markers, >1,300 plants). We observed dramatic differences between male and female map lengths that were calculated as 88 cM and 52 cM, respectively. This difference is remarkably parallel to that between the total synaptonemal complex lengths measured in male and female meiocytes by immunolabeling of ZYP1 (a component of the synaptonemal complex). Moreover, CO landscapes were clearly different: in particular, at both ends of the map, male CO rates were higher (up to 4-fold the mean value), whereas female CO rates were equal or even below the chromosomal average. This unique material gave us the opportunity to perform a detailed analysis of CO interference on Chromosome 4 in male and female meiosis. The number of COs per chromosome and the distances between them clearly departs from randomness. Strikingly, the interference level (measured by coincidence) varied significantly along the chromosome in male meiosis and was correlated to the physical distance between COs. The significance of this finding on the relevance of current CO interference models is discussed.

Figure 1. Variation of CO Rates along A. thaliana Chromosome 4

(A) CO rates in F2 population (green) and the pool of male and female backcross populations (red). (B) Alignment of physical map (center) and both male (top) and female (bottom) genetic maps. (C) CO rates in male (blue) and female (pink) populations. Orange stars mark the intervals that are significantly different between both populations (p-values < 0.02). A schematic representation of Chromosome 4 is aligned with the physical map and each CO plot, which includes 5-Mb scale coordinates, centromere (diamond), heterochromatic knob (gray box), nucleolar organizer region (NOR, black box).

Figure 2. Coimmunolocalization of ASY1 (Red) and ZYP1 (Green) in Male and Female Meiocytes at Pachytene Stage

Bar = 10 μm.

Figure 3. Distributions of CO Number per Chromosome 4

Bars represent the frequency of chromatids with 0, 1, 2, or 3 COs. (A) Observed (blue) and Poisson (purple) distributions in M population. (B) Observed (blue) and Poisson (purple) distributions in F population. Corresponding number of chromatids is indicated above each bar.

Figure 4. Double-CO Locations on (A) Male and (B) Female Chromosome 4

All double-COs on chromosomes harboring exactly two COs were plotted in two-dimensional graphs. The x and y axis values indicate the genetic position (relative to the nucleolar organizing region) of the first and the second CO, respectively. The diagonal line and the upper left corner correspond to minimal (null) and maximal (chromosome-wide) inter-COs distances, respectively.

Figure 5. Distributions of Inter-CO Distances on Chromosome 4

Observed (blue) and random (purple) distributions of inter-CO distances in (A) F and (B) M populations.

Figure 6. C3 Coincidence Plots along the (A) Male or (B) Female Chromosome 4

All possible pairs of adjacent intervals (each being 17.5 cM ± 5%) were used for calculation of coefficient of coincidence, defined as the frequency of double-COs divided by the frequencies of COs in both intervals (see Materials and Methods). These C3 coincidence values were plotted against the genetic position of the junction between the two adjacent intervals. Blue and pink dots represent, respectively, M and F datasets. Numbered green dots mark the pairs of intervals used for statistical comparison of C3 coincidence values. Error bar for these dots correspond to the standard deviation of coincidence calculated according to [35]. Each plot is aligned with the corresponding genetic map, the physical map, and a schematic representation of the chromosome, which includes 5-Mb scale coordinates, centromere (diamond), heterochromatic knob (gray box), nucleolar organizer region (NOR, black box).

Figure 7. C4 Coincidence Plots along the Male Chromosome 4

All possible combinations between a fixed and a nonoverlapping interval (each being 17.5 cM ± 5%) were used for calculation of coefficient of coincidence, defined as the frequency of double-COs divided by the frequencies of COs in both intervals (see Materials and Methods). These C4 coincidence values were plotted against the genetic distance between the centers of the intervals. The fixed interval is located at the end of either (A) the short arm or (B) the long arm. Each plot is aligned with the corresponding genetic map, the physical map, and a schematic representation of the chromosome, which includes 5-Mb scale coordinates, centromere (diamond), heterochromatic knob (gray box), nucleolar organizer region (NOR, black box). For both plots, abscissa values indicate the genetic distance between the centers of the fixed and the “moving” intervals. The red two-headed arrow indicates the fixed interval position.

Figure 8. C4 Coincidence Plots along the Female Chromosome 4

All possible combinations between a fixed and a nonoverlapping interval (each being 17.5 cM ± 5%) were used for calculation of coefficient of coincidence, defined as the frequency of double-COs divided by the frequencies of COs in both intervals (see Materials and Methods). These C4 coincidence values were plotted against the genetic distance between the centers of the intervals. The fixed interval is located at the end of either (A) the short arm or (B) the long arm. Each plot is aligned with the corresponding genetic map, the physical map, and a schematic representation of the chromosome, which includes 5-Mb scale coordinates, centromere (diamond), heterochromatic knob (gray box), nucleolar organizer region (NOR, black box). For both plots, abscissa values indicate the genetic distance between the centers of the fixed and the “moving” interval. The red two-headed arrow indicates the fixed interval position.

Figure 9. Scatter Plot between C3 Coincidence Value and Physical Size for Male Chromosome 4

Violet dots correspond to pairs of intervals encompassing the heterochromatic knob and the centromere, while orange dots correspond to the remaining pairs of intervals (all located on the long arm). Numbered green dots represent the same pairs of intervals than those represented in Figure 6A and used for the comparisons of C3 coincidence values. (A) Physical sizes were calculated from genome sequence data (Build 6 version 0), adding if necessary 1.5 Mb to take account for the centromere. (B) Cumulated centromere and knob size (4.7 Mb) was subtracted from the size of the relevant pairs of intervals.